Header list of 1klr.pdb file
Complete list - t 27 2 Bytes
HEADER TRANSCRIPTION 12-DEC-01 1KLR
TITLE NMR STRUCTURE OF THE ZFY-6T[Y10F] ZINC FINGER
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ZINC FINGER Y-CHROMOSOMAL PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: THIS PEPTIDE WAS SYNTHESIZED BY SOLID-PHASE
SOURCE 4 SYNTHESIS. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO
SOURCE 5 SAPIENS (HUMAN).
KEYWDS ZINC FINGER, TRANSCRIPTION
EXPDTA SOLUTION NMR
NUMMDL 25
AUTHOR M.J.LACHENMANN,J.E.LADBURY,N.B.PHILLIPS,N.NARAYANA,X.QIAN,M.A.WEISS
REVDAT 3 27-OCT-21 1KLR 1 REMARK SEQADV LINK
REVDAT 2 24-FEB-09 1KLR 1 VERSN
REVDAT 1 13-MAR-02 1KLR 0
JRNL AUTH M.J.LACHENMANN,J.E.LADBURY,N.B.PHILLIPS,N.NARAYANA,X.QIAN,
JRNL AUTH 2 M.A.WEISS
JRNL TITL THE HIDDEN THERMODYNAMICS OF A ZINC FINGER.
JRNL REF J.MOL.BIOL. V. 316 969 2002
JRNL REFN ISSN 0022-2836
JRNL PMID 11884136
JRNL DOI 10.1006/JMBI.2001.5335
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH X.QIAN,M.A.WEISS
REMARK 1 TITL TWO-DIMENSIONAL NMR STUDIES OF THE ZINC FINGER MOTIF:
REMARK 1 TITL 2 SOLUTION STRUCTURES AND DYNAMICS OF MUTANT ZFY DOMAINS
REMARK 1 TITL 3 CONTAINING AROMATIC SUBSTITUTIONS IN THE HYDROPHOBIC CORE
REMARK 1 REF BIOCHEMISTRY V. 31 7463 1992
REMARK 1 REFN ISSN 0006-2960
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : VNMR 4.3-5.3, X-PLOR 3.1
REMARK 3 AUTHORS : VARIAN, INC. (VNMR), BRUNGER, A.T. (X-PLOR)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 STRUCTURES ARE BASED ON 229 INTERRESIDUE
REMARK 3 NOE-DERIVED DISTANCE CONSTRAINTS, 24 DIHEDRAL
REMARK 3 ANGLE RESTRAINTS, AND 10 HYDROGEN BOND RESTRAINTS.
REMARK 4
REMARK 4 1KLR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-01.
REMARK 100 THE DEPOSITION ID IS D_1000015086.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298; 298
REMARK 210 PH : 6.0; 6.0
REMARK 210 IONIC STRENGTH : 50MM D11-TRIS-HCL, 2.2MM ZNCL2;
REMARK 210 50MM D11-TRIS-HCL, 5.5MM ZNCL2
REMARK 210 PRESSURE : AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 2MM ZFY-6T[Y10F]; 2MM ZFY
REMARK 210 -6T[Y10F]; 5MM ZFY-6T[Y10F]; 5MM
REMARK 210 ZFY-6T[Y10F]
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 3D-TOCSY
REMARK 210 -NOESY; 2D-ROESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ
REMARK 210 SPECTROMETER MODEL : VXRS; UNITYPLUS; INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NHFIT, DGII STANDALONE, VNMR 4.3
REMARK 210 -5.3
REMARK 210 METHOD USED : DISTANCE GEOMETRY/SIMULATED
REMARK 210 ANNEALING, FOLLOWED BY
REMARK 210 RESTRAINED MOLECULAR DYNAMICS.
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 52
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 14
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING
REMARK 210 2D AND 3D HOMONUCLEAR TECHNIQUES.
REMARK 210 THIS STRUCTURE REPRESENTS A REFINEMENT OF
REMARK 210 THE STRUCTURE ORIGINALLY PUBLISHED IN
REMARK 210 SECONDARY CITATION #1 (QIAN, X. AND WEISS,
REMARK 210 M.A.). ADDITIONAL CONSTRAINTS WERE DETERMINED
REMARK 210 USING HIGHER-CONCENTRATION SAMPLES AND BY
REMARK 210 HOMONUCLEAR 3D-NMR METHODS.
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
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 12 SER A 16 N - CA - C ANGL. DEV. = -17.5 DEGREES
REMARK 500 13 SER A 16 N - CA - C ANGL. DEV. = 19.0 DEGREES
REMARK 500 14 ARG A 11 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
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 TYR A 7 -56.38 -137.71
REMARK 500 1 CYS A 8 -160.43 -125.09
REMARK 500 1 GLU A 9 57.06 -103.55
REMARK 500 1 LYS A 28 -103.18 -98.97
REMARK 500 2 TYR A 7 -53.61 -131.83
REMARK 500 2 CYS A 8 -158.03 -124.04
REMARK 500 2 GLU A 9 55.65 -105.35
REMARK 500 2 SER A 15 -54.82 111.13
REMARK 500 2 LYS A 28 -58.66 109.19
REMARK 500 2 GLU A 29 66.82 12.59
REMARK 500 3 GLN A 6 43.62 -95.95
REMARK 500 3 TYR A 7 -54.68 -129.02
REMARK 500 3 CYS A 8 -164.24 -126.24
REMARK 500 3 GLU A 9 61.71 -107.25
REMARK 500 3 SER A 12 -24.14 -140.11
REMARK 500 3 ALA A 13 45.82 33.46
REMARK 500 3 ASP A 14 -61.07 -126.18
REMARK 500 3 SER A 15 -65.15 111.97
REMARK 500 3 LYS A 28 72.66 8.88
REMARK 500 4 GLN A 6 -35.44 116.67
REMARK 500 4 CYS A 8 -165.83 -113.25
REMARK 500 4 GLU A 9 50.93 -100.02
REMARK 500 4 ASP A 14 -69.63 -122.41
REMARK 500 4 SER A 15 -58.61 115.20
REMARK 500 4 LYS A 28 70.39 8.60
REMARK 500 5 TYR A 7 -50.76 -129.20
REMARK 500 5 CYS A 8 -164.96 -119.80
REMARK 500 5 GLU A 9 57.73 -108.68
REMARK 500 5 SER A 12 -65.13 -143.07
REMARK 500 5 ALA A 13 26.73 118.73
REMARK 500 5 SER A 27 -57.05 -137.52
REMARK 500 5 GLU A 29 -65.62 -7.97
REMARK 500 6 TYR A 7 -57.55 -140.96
REMARK 500 6 CYS A 8 -137.08 -116.76
REMARK 500 6 PHE A 10 118.27 -13.69
REMARK 500 6 HIS A 26 -73.55 -121.58
REMARK 500 7 TYR A 7 -58.71 -131.06
REMARK 500 7 CYS A 8 -154.94 -118.29
REMARK 500 7 GLU A 9 54.11 -109.45
REMARK 500 7 SER A 16 117.30 131.73
REMARK 500 7 ASN A 17 48.58 -88.16
REMARK 500 7 HIS A 26 -52.00 -123.12
REMARK 500 7 SER A 27 -146.71 -115.60
REMARK 500 7 LYS A 28 64.70 6.70
REMARK 500 7 GLU A 29 115.51 104.62
REMARK 500 8 TYR A 7 -58.48 -136.75
REMARK 500 8 CYS A 8 -161.60 -115.59
REMARK 500 8 GLU A 9 57.52 -109.86
REMARK 500 8 SER A 15 -61.60 117.98
REMARK 500 9 TYR A 7 -54.51 -136.82
REMARK 500
REMARK 500 THIS ENTRY HAS 152 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 11 0.31 SIDE CHAIN
REMARK 500 2 ARG A 11 0.23 SIDE CHAIN
REMARK 500 3 ARG A 11 0.29 SIDE CHAIN
REMARK 500 4 ARG A 11 0.25 SIDE CHAIN
REMARK 500 5 ARG A 11 0.30 SIDE CHAIN
REMARK 500 6 ARG A 11 0.28 SIDE CHAIN
REMARK 500 7 ARG A 11 0.20 SIDE CHAIN
REMARK 500 8 ARG A 11 0.28 SIDE CHAIN
REMARK 500 9 ARG A 11 0.26 SIDE CHAIN
REMARK 500 10 ARG A 11 0.14 SIDE CHAIN
REMARK 500 11 ARG A 11 0.25 SIDE CHAIN
REMARK 500 12 ARG A 11 0.31 SIDE CHAIN
REMARK 500 13 ARG A 11 0.31 SIDE CHAIN
REMARK 500 14 ARG A 11 0.31 SIDE CHAIN
REMARK 500 15 ARG A 11 0.31 SIDE CHAIN
REMARK 500 16 ARG A 11 0.29 SIDE CHAIN
REMARK 500 17 ARG A 11 0.26 SIDE CHAIN
REMARK 500 18 ARG A 11 0.28 SIDE CHAIN
REMARK 500 19 ARG A 11 0.31 SIDE CHAIN
REMARK 500 20 ARG A 11 0.17 SIDE CHAIN
REMARK 500 21 ARG A 11 0.08 SIDE CHAIN
REMARK 500 22 ARG A 11 0.30 SIDE CHAIN
REMARK 500 23 ARG A 11 0.25 SIDE CHAIN
REMARK 500 24 ARG A 11 0.31 SIDE CHAIN
REMARK 500 25 ARG A 11 0.31 SIDE CHAIN
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 ZN A 31 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 5 SG
REMARK 620 2 CYS A 8 SG 111.4
REMARK 620 3 HIS A 21 NE2 109.6 111.5
REMARK 620 4 HIS A 26 NE2 106.1 111.2 106.8
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 31
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5ZNF RELATED DB: PDB
REMARK 900 5ZNF CONTAINS THE WILD-TYPE ZFY-6T ZINC FINGER
REMARK 900 RELATED ID: 1KLS RELATED DB: PDB
REMARK 900 1KLS CONTAINS THE Y10L MUTANT
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 THE MUTATION Y10F WAS CREATED FOR STRUCTURAL
REMARK 999 STUDIES. IN ADDITION, THE P2T MUTATION AND
REMARK 999 C-TERMINAL K, ORIGINALLY INTRODUCED IN ZFY-6T
REMARK 999 (PDB ENTRY 5ZNF) IMPROVE SAMPLE BEHAVIOR
REMARK 999 WITHOUT AFFECTING STRUCTURE.
DBREF 1KLR A 1 29 UNP P08048 ZFY_HUMAN 570 598
SEQADV 1KLR THR A 2 UNP P08048 PRO 571 ENGINEERED MUTATION
SEQADV 1KLR PHE A 10 UNP P08048 TYR 579 ENGINEERED MUTATION
SEQADV 1KLR LYS A 30 UNP P08048 SEE REMARK 999
SEQRES 1 A 30 LYS THR TYR GLN CYS GLN TYR CYS GLU PHE ARG SER ALA
SEQRES 2 A 30 ASP SER SER ASN LEU LYS THR HIS ILE LYS THR LYS HIS
SEQRES 3 A 30 SER LYS GLU LYS
HET ZN A 31 1
HETNAM ZN ZINC ION
FORMUL 2 ZN ZN 2+
HELIX 1 1 SER A 15 HIS A 26 1 12
LINK SG CYS A 5 ZN ZN A 31 1555 1555 2.30
LINK SG CYS A 8 ZN ZN A 31 1555 1555 2.30
LINK NE2 HIS A 21 ZN ZN A 31 1555 1555 2.00
LINK NE2 HIS A 26 ZN ZN A 31 1555 1555 2.00
CISPEP 1 SER A 16 ASN A 17 7 0.76
CISPEP 2 SER A 15 SER A 16 10 -0.09
CISPEP 3 SER A 16 ASN A 17 10 0.81
CISPEP 4 LYS A 23 THR A 24 10 0.55
CISPEP 5 SER A 27 LYS A 28 10 0.48
CISPEP 6 SER A 16 ASN A 17 12 1.25
CISPEP 7 SER A 15 SER A 16 13 0.39
CISPEP 8 LYS A 1 THR A 2 20 0.09
CISPEP 9 SER A 27 LYS A 28 20 -0.23
CISPEP 10 LYS A 1 THR A 2 21 -0.02
CISPEP 11 LYS A 23 THR A 24 22 0.42
CISPEP 12 LYS A 1 THR A 2 24 0.01
SITE 1 AC1 4 CYS A 5 CYS A 8 HIS A 21 HIS A 26
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 - t 27 2 Bytes