Header list of 1f55.pdb file
Complete list - b 16 2 Bytes
HEADER TRANSPORT PROTEIN 13-JUN-00 1F55
TITLE SOLUTION STRUCTURE OF THE CALCIUM BOUND N-TERMINAL DOMAIN OF YEAST
TITLE 2 CALMODULIN
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CALMODULIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: N-TERMINAL DOMAIN;
COMPND 5 ENGINEERED: YES;
COMPND 6 OTHER_DETAILS: INTRACELLULAR CALCIUM SENSOR
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE;
SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST;
SOURCE 4 ORGANISM_TAXID: 4932;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-30B(+) AND PIC10
KEYWDS EF-HAND, HELIX-LOOP-HELIX, TRANSPORT PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 30
AUTHOR H.ISHIDA,K.TAKAHASHI,K.NAKASHIMA,Y.KUMAKI,M.NAKATA,K.HIKICHI,M.YAZAWA
REVDAT 3 16-FEB-22 1F55 1 REMARK LINK
REVDAT 2 24-FEB-09 1F55 1 VERSN
REVDAT 1 15-JUL-03 1F55 0
JRNL AUTH H.ISHIDA,K.TAKAHASHI,K.NAKASHIMA,Y.KUMAKI,M.NAKATA,
JRNL AUTH 2 K.HIKICHI,M.YAZAWA
JRNL TITL SOLUTION STRUCTURES OF THE N-TERMINAL DOMAIN OF YEAST
JRNL TITL 2 CALMODULIN: CA2+-DEPENDENT CONFORMATIONAL CHANGE AND ITS
JRNL TITL 3 FUNCTIONAL IMPLICATION
JRNL REF BIOCHEMISTRY V. 39 13660 2000
JRNL REFN ISSN 0006-2960
JRNL PMID 11076504
JRNL DOI 10.1021/BI000582X
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR 3.851, X-PLOR 3.851
REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 920 RESTRAINTS, 863 ARE NOE-
REMARK 3 DERIVED
REMARK 3 DISTANCE CONSTRAINTS, 17 DIHEDRAL ANGLE RESTRAINTS, 28 DISTANCE
REMARK 3 RESTRAINTS
REMARK 3 FROM HYDROGEN BONDS, 12 CALCIUM-LIGAND DISTANCE RESTRAINTS
REMARK 4
REMARK 4 1F55 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-00.
REMARK 100 THE DEPOSITION ID IS D_1000011255.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303
REMARK 210 PH : 6.8
REMARK 210 IONIC STRENGTH : 50MM KCL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 5 MM N-TERMINAL DOMAIN OF YEAST
REMARK 210 CALMODULIN; 50 MM KCL; 15 MM
REMARK 210 CACL2; 90% H2O, 10% D2O; 3 MM N-
REMARK 210 TERMINAL DOMAIN OF YEAST
REMARK 210 CALMODULIN U-15N; 50 MM KCL; 9
REMARK 210 MM CACL2; 90% H2O, 10% D2O; 3 MM
REMARK 210 N-TERMINAL DOMAIN OF YEAST
REMARK 210 CALMODULIN; 50 MM KCL; 9 MM
REMARK 210 CACL2; 99.99% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 2D TOCSY;
REMARK 210 3D_15N-SEPARATED_NOESY; 3D_15N-
REMARK 210 SEPARATED_TOCSY; 15N-HSQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : A
REMARK 210 SPECTROMETER MANUFACTURER : JEOL
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 200
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING DOUBLE-RESONANCE NMR
REMARK 210 SPECTROSCOPY ON 15N-LABELED PROTEIN
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O LEU A 4 HG1 THR A 5 1.51
REMARK 500 O PHE A 12 H PHE A 16 1.56
REMARK 500 OD1 ASP A 20 H ASP A 22 1.59
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 1 LEU A 4 -108.97 -115.68
REMARK 500 1 THR A 5 -144.35 49.76
REMARK 500 1 LEU A 41 -42.98 -144.10
REMARK 500 1 ASP A 56 90.35 -64.15
REMARK 500 1 PHE A 65 -71.35 -44.71
REMARK 500 1 MET A 72 -92.00 -58.95
REMARK 500 1 ARG A 74 -142.22 61.07
REMARK 500 1 GLN A 75 -46.06 -163.76
REMARK 500 1 LEU A 76 -76.24 -132.55
REMARK 500 2 LEU A 4 -119.42 -92.82
REMARK 500 2 THR A 5 -145.08 52.24
REMARK 500 2 ASP A 22 20.02 -155.38
REMARK 500 2 ASN A 23 29.78 42.23
REMARK 500 2 SER A 28 -158.77 -106.13
REMARK 500 2 GLU A 31 -71.32 -42.34
REMARK 500 2 SER A 42 64.15 -176.92
REMARK 500 2 ASP A 56 95.28 -56.22
REMARK 500 2 PHE A 65 -71.33 -43.32
REMARK 500 2 SER A 66 -35.12 -34.93
REMARK 500 2 MET A 72 -90.07 -51.66
REMARK 500 2 ARG A 74 129.79 61.47
REMARK 500 2 GLN A 75 -54.63 -143.48
REMARK 500 2 LEU A 76 175.25 -47.56
REMARK 500 3 ASN A 3 94.53 57.47
REMARK 500 3 LEU A 4 -106.35 -81.54
REMARK 500 3 THR A 5 -146.17 51.40
REMARK 500 3 ASP A 22 20.53 -162.91
REMARK 500 3 ASN A 23 27.14 41.40
REMARK 500 3 LEU A 39 -62.71 -134.70
REMARK 500 3 SER A 42 48.32 -158.15
REMARK 500 3 SER A 44 145.71 69.53
REMARK 500 3 ASN A 60 34.34 -97.60
REMARK 500 3 HIS A 61 13.82 58.36
REMARK 500 3 PHE A 65 -70.07 -50.28
REMARK 500 3 MET A 72 -79.61 -68.50
REMARK 500 3 GLN A 75 -147.09 64.26
REMARK 500 4 ASN A 3 -145.79 -128.46
REMARK 500 4 LEU A 4 -115.13 -84.73
REMARK 500 4 THR A 5 -145.98 52.04
REMARK 500 4 SER A 29 -87.20 -53.22
REMARK 500 4 GLU A 31 -79.05 -42.66
REMARK 500 4 LEU A 41 172.90 -54.65
REMARK 500 4 SER A 44 147.02 67.67
REMARK 500 4 PHE A 65 -71.11 -58.05
REMARK 500 4 MET A 72 -80.54 -61.54
REMARK 500 4 SER A 73 164.03 -44.24
REMARK 500 5 SER A 2 -74.29 -144.37
REMARK 500 5 LEU A 4 -134.03 -114.87
REMARK 500 5 THR A 5 -142.30 50.33
REMARK 500 5 ASP A 22 26.48 -172.41
REMARK 500
REMARK 500 THIS ENTRY HAS 368 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 1 ARG A 37 0.15 SIDE CHAIN
REMARK 500 1 ARG A 74 0.30 SIDE CHAIN
REMARK 500 2 ARG A 37 0.23 SIDE CHAIN
REMARK 500 2 ARG A 74 0.27 SIDE CHAIN
REMARK 500 3 ARG A 37 0.29 SIDE CHAIN
REMARK 500 3 ARG A 74 0.28 SIDE CHAIN
REMARK 500 4 ARG A 37 0.23 SIDE CHAIN
REMARK 500 4 ARG A 74 0.30 SIDE CHAIN
REMARK 500 5 ARG A 37 0.17 SIDE CHAIN
REMARK 500 5 ARG A 74 0.24 SIDE CHAIN
REMARK 500 6 ARG A 37 0.31 SIDE CHAIN
REMARK 500 6 ARG A 74 0.20 SIDE CHAIN
REMARK 500 7 ARG A 37 0.29 SIDE CHAIN
REMARK 500 7 ARG A 74 0.32 SIDE CHAIN
REMARK 500 8 ARG A 37 0.30 SIDE CHAIN
REMARK 500 8 ARG A 74 0.30 SIDE CHAIN
REMARK 500 9 ARG A 37 0.32 SIDE CHAIN
REMARK 500 9 ARG A 74 0.20 SIDE CHAIN
REMARK 500 10 ARG A 37 0.25 SIDE CHAIN
REMARK 500 10 ARG A 74 0.22 SIDE CHAIN
REMARK 500 11 ARG A 37 0.28 SIDE CHAIN
REMARK 500 11 ARG A 74 0.15 SIDE CHAIN
REMARK 500 12 ARG A 37 0.22 SIDE CHAIN
REMARK 500 12 ARG A 74 0.31 SIDE CHAIN
REMARK 500 13 ARG A 37 0.32 SIDE CHAIN
REMARK 500 13 ARG A 74 0.26 SIDE CHAIN
REMARK 500 14 ARG A 37 0.28 SIDE CHAIN
REMARK 500 14 ARG A 74 0.24 SIDE CHAIN
REMARK 500 15 ARG A 37 0.23 SIDE CHAIN
REMARK 500 15 ARG A 74 0.31 SIDE CHAIN
REMARK 500 16 ARG A 37 0.28 SIDE CHAIN
REMARK 500 16 ARG A 74 0.26 SIDE CHAIN
REMARK 500 17 ARG A 37 0.21 SIDE CHAIN
REMARK 500 17 ARG A 74 0.28 SIDE CHAIN
REMARK 500 18 ARG A 37 0.32 SIDE CHAIN
REMARK 500 18 ARG A 74 0.21 SIDE CHAIN
REMARK 500 19 ARG A 37 0.20 SIDE CHAIN
REMARK 500 19 ARG A 74 0.23 SIDE CHAIN
REMARK 500 20 ARG A 37 0.17 SIDE CHAIN
REMARK 500 20 ARG A 74 0.28 SIDE CHAIN
REMARK 500 21 ARG A 37 0.28 SIDE CHAIN
REMARK 500 21 ARG A 74 0.15 SIDE CHAIN
REMARK 500 22 ARG A 37 0.31 SIDE CHAIN
REMARK 500 22 ARG A 74 0.31 SIDE CHAIN
REMARK 500 23 ARG A 37 0.13 SIDE CHAIN
REMARK 500 23 ARG A 74 0.20 SIDE CHAIN
REMARK 500 24 ARG A 37 0.09 SIDE CHAIN
REMARK 500 24 ARG A 74 0.28 SIDE CHAIN
REMARK 500 25 ARG A 37 0.08 SIDE CHAIN
REMARK 500 25 ARG A 74 0.20 SIDE CHAIN
REMARK 500
REMARK 500 THIS ENTRY HAS 60 PLANE DEVIATIONS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 101 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 20 OD2
REMARK 620 2 ASP A 20 OD1 40.9
REMARK 620 3 ASP A 22 OD2 115.7 76.7
REMARK 620 4 ASN A 24 OD1 102.0 108.9 81.1
REMARK 620 5 SER A 26 O 51.6 72.3 134.8 140.0
REMARK 620 6 GLU A 31 OE1 103.5 84.1 78.2 152.2 66.7
REMARK 620 7 GLU A 31 OE2 86.6 49.3 49.2 126.7 85.6 45.2
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CA A 102 CA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 56 OD1
REMARK 620 2 ASP A 58 OD2 78.0
REMARK 620 3 ASP A 58 OD1 52.0 43.3
REMARK 620 4 ASN A 60 OD1 49.4 58.1 70.9
REMARK 620 5 ASN A 60 ND2 92.4 53.3 92.0 43.4
REMARK 620 6 GLN A 62 O 52.0 109.9 103.0 52.2 80.2
REMARK 620 7 GLU A 67 OE1 84.7 123.2 84.1 134.0 176.0 100.0
REMARK 620 8 GLU A 67 OE2 119.7 99.5 85.1 155.0 134.3 144.8 46.1
REMARK 620 N 1 2 3 4 5 6 7
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 101
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 102
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1F54 RELATED DB: PDB
REMARK 900 1F54 IS THE APO-FORM OF THE SAME PROTEIN
DBREF 1F55 A 1 77 UNP P06787 CALM_YEAST 2 78
SEQRES 1 A 77 SER SER ASN LEU THR GLU GLU GLN ILE ALA GLU PHE LYS
SEQRES 2 A 77 GLU ALA PHE ALA LEU PHE ASP LYS ASP ASN ASN GLY SER
SEQRES 3 A 77 ILE SER SER SER GLU LEU ALA THR VAL MET ARG SER LEU
SEQRES 4 A 77 GLY LEU SER PRO SER GLU ALA GLU VAL ASN ASP LEU MET
SEQRES 5 A 77 ASN GLU ILE ASP VAL ASP GLY ASN HIS GLN ILE GLU PHE
SEQRES 6 A 77 SER GLU PHE LEU ALA LEU MET SER ARG GLN LEU LYS
HET CA A 101 1
HET CA A 102 1
HETNAM CA CALCIUM ION
FORMUL 2 CA 2(CA 2+)
HELIX 1 1 THR A 5 ASP A 20 1 16
HELIX 2 2 SER A 29 LEU A 41 1 13
HELIX 3 3 SER A 44 ASP A 56 1 13
HELIX 4 4 PHE A 65 MET A 72 1 8
SHEET 1 A 2 SER A 26 SER A 28 0
SHEET 2 A 2 GLN A 62 GLU A 64 -1 O ILE A 63 N ILE A 27
LINK OD2 ASP A 20 CA CA A 101 1555 1555 3.25
LINK OD1 ASP A 20 CA CA A 101 1555 1555 2.80
LINK OD2 ASP A 22 CA CA A 101 1555 1555 2.81
LINK OD1 ASN A 24 CA CA A 101 1555 1555 2.82
LINK O SER A 26 CA CA A 101 1555 1555 2.81
LINK OE1 GLU A 31 CA CA A 101 1555 1555 2.80
LINK OE2 GLU A 31 CA CA A 101 1555 1555 2.81
LINK OD1 ASP A 56 CA CA A 102 1555 1555 2.80
LINK OD2 ASP A 58 CA CA A 102 1555 1555 3.13
LINK OD1 ASP A 58 CA CA A 102 1555 1555 2.48
LINK OD1 ASN A 60 CA CA A 102 1555 1555 2.79
LINK ND2 ASN A 60 CA CA A 102 1555 1555 3.07
LINK O GLN A 62 CA CA A 102 1555 1555 2.48
LINK OE1 GLU A 67 CA CA A 102 1555 1555 2.78
LINK OE2 GLU A 67 CA CA A 102 1555 1555 2.73
SITE 1 AC1 5 ASP A 20 ASP A 22 ASN A 24 SER A 26
SITE 2 AC1 5 GLU A 31
SITE 1 AC2 6 ASP A 56 ASP A 58 ASN A 60 GLN A 62
SITE 2 AC2 6 ILE A 63 GLU A 67
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
Complete list - b 16 2 Bytes