Header list of 1nvo.pdb file
Complete list - b 23 2 Bytes
HEADER UNKNOWN FUNCTION 04-FEB-03 1NVO
TITLE SOLUTION STRUCTURE OF A FOUR-HELIX BUNDLE MODEL, APO-DF1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HOMODIMERIC ALPHA2 FOUR-HELIX BUNDLE;
COMPND 3 CHAIN: A, B;
COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 OTHER_DETAILS: CHEMICALLY SYNTHESIZED
KEYWDS DE NOVO PROTEIN DESIGN, ALPHA-HELICAL BUNDLE, DIIRON PROTEIN MODEL,
KEYWDS 2 UNKNOWN FUNCTION
EXPDTA SOLUTION NMR
NUMMDL 14
AUTHOR O.MAGLIO,F.NASTRI,V.PAVONE,A.LOMBARDI,W.F.DEGRADO
REVDAT 5 23-FEB-22 1NVO 1 REMARK LINK
REVDAT 4 24-FEB-09 1NVO 1 VERSN
REVDAT 3 13-JAN-04 1NVO 1 JRNL
REVDAT 2 02-APR-03 1NVO 1 JRNL
REVDAT 1 25-MAR-03 1NVO 0
JRNL AUTH O.MAGLIO,F.NASTRI,V.PAVONE,A.LOMBARDI,W.F.DEGRADO
JRNL TITL PREORGANIZATION OF MOLECULAR BINDING SITES IN DESIGNED
JRNL TITL 2 DIIRON PROTEINS
JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 3772 2003
JRNL REFN ISSN 0027-8424
JRNL PMID 12655072
JRNL DOI 10.1073/PNAS.0730771100
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH A.LOMBARDI,C.M.SUMMA,S.GEREMIA,L.RANDACCIO,V.PAVONE,
REMARK 1 AUTH 2 W.F.DEGRADO
REMARK 1 TITL RETROSTRUCTURAL ANALYSIS OF METALLOPROTEINS. APPLICATION TO
REMARK 1 TITL 2 THE DESIGN OF A MINIMAL MODEL FOR DIIRON PROTEINS
REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 97 6298 2000
REMARK 1 REFN ISSN 0027-8424
REMARK 1 DOI 10.1073/PNAS.97.12.6298
REMARK 1 REFERENCE 2
REMARK 1 AUTH C.M.SUMMA,A.LOMBARDI,M.LEWIS,W.F.DEGRADO
REMARK 1 TITL TERTIARY TEMPLATES FOR THE DESIGN OF DIIRON PROTEIN
REMARK 1 REF CURR.OPIN.STRUCT.BIOL. V. 9 500 1999
REMARK 1 REFN ISSN 0959-440X
REMARK 1 DOI 10.1016/S0959-440X(99)80071-2
REMARK 1 REFERENCE 3
REMARK 1 AUTH L.DI COSTANZO,H.WADE,S.GEREMIA,L.RANDACCIO,V.PAVONE,
REMARK 1 AUTH 2 W.F.DEGRADO,A.LOMBARDI
REMARK 1 TITL TOWARD THE DE NOVO DESIGN OF A CATALYTICALLY ACTIVE HELIX
REMARK 1 TITL 2 BUNDLE: A SUBSTRATE-ACCESSIBLE CARBOXYLATE-BRIDGED DINUCLEAR
REMARK 1 TITL 3 METAL CENTER
REMARK 1 REF J.AM.CHEM.SOC. V. 123 12749 2001
REMARK 1 REFN ISSN 0002-7863
REMARK 1 DOI 10.1021/JA010506X
REMARK 1 REFERENCE 4
REMARK 1 AUTH W.F.DEGRADO,L.DI COSTANZO,S.GEREMIA,A.LOMBARDI,V.PAVONE,
REMARK 1 AUTH 2 L.RANDACCIO
REMARK 1 TITL SLIDING HELIX AND CHANGE OF COORDINATION GEOMETRY IN A MODEL
REMARK 1 TITL 2 DI-MN(II) PROTEIN
REMARK 1 REF ANGEW.CHEM.INT.ED.ENGL. V. 42 417 2003
REMARK 1 REFN ESSN 0570-0833
REMARK 1 DOI 10.1002/ANIE.200390127
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : NMRPIPE, AMBER 7.0
REMARK 3 AUTHORS : DELAGLIO ET AL. (NMRPIPE), CASE ET AL. (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1NVO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-03.
REMARK 100 THE DEPOSITION ID IS D_1000018255.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 4.0
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.0 MM PROTEIN CONCENTRATION;
REMARK 210 90% H2O, 10% DMSO
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D TOCSY; 2D NOESY; DQF-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : DYANA 1.5
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS,
REMARK 210 SIMULATED ANNEALING, ENERGY
REMARK 210 RESTRAINED MINIMIZATION
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 40
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 14
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE
REMARK 210 COVALENT GEOMETRY,STRUCTURES
REMARK 210 WITH FAVORABLE NON-BOND ENERGY,
REMARK 210 STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS,STRUCTURES
REMARK 210 WITH THE LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D
REMARK 210 HOMONUCLEAR TECHNIQUES
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: DIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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: 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 1 TYR A 2 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES
REMARK 500 6 TYR A 2 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 8 TYR A 2 CB - CG - CD2 ANGL. DEV. = -3.8 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 LEU A 7 -43.46 -131.33
REMARK 500 1 GLU A 44 27.56 -75.92
REMARK 500 1 THR A 45 -51.01 -148.30
REMARK 500 1 LEU A 47 -54.14 72.53
REMARK 500 1 LEU B 7 -61.79 -145.59
REMARK 500 2 TYR A 2 -55.35 -19.10
REMARK 500 2 LEU A 6 37.51 -95.19
REMARK 500 2 LEU A 7 -57.83 -144.51
REMARK 500 2 ILE A 46 -58.31 -26.25
REMARK 500 2 LEU A 47 134.02 -170.71
REMARK 500 2 TYR B 2 -69.76 -26.81
REMARK 500 2 LEU B 7 -66.45 -151.39
REMARK 500 2 GLU B 44 35.75 -76.86
REMARK 500 2 THR B 45 -48.27 -150.22
REMARK 500 2 ILE B 46 66.22 36.21
REMARK 500 3 LEU A 7 -51.95 -130.99
REMARK 500 3 ILE A 46 67.55 35.67
REMARK 500 3 LEU A 47 16.20 57.87
REMARK 500 3 GLU B 5 -50.24 -137.44
REMARK 500 4 GLU A 5 -63.33 -102.59
REMARK 500 4 LEU A 6 33.97 -83.67
REMARK 500 4 LEU A 7 -55.47 -143.66
REMARK 500 4 GLU B 5 -74.07 -102.28
REMARK 500 4 LEU B 47 -138.47 64.63
REMARK 500 5 LEU A 7 -47.78 -135.67
REMARK 500 5 LYS A 25 63.99 61.69
REMARK 500 5 THR A 45 -46.43 -152.71
REMARK 500 5 LEU A 47 79.80 62.87
REMARK 500 5 LEU B 7 -62.66 -133.60
REMARK 500 5 GLU B 44 27.30 -75.47
REMARK 500 5 THR B 45 -45.46 -150.16
REMARK 500 5 ILE B 46 49.20 39.80
REMARK 500 6 LEU A 7 -58.09 -160.58
REMARK 500 6 GLU B 5 -69.46 -127.28
REMARK 500 6 LEU B 7 -53.77 -140.20
REMARK 500 6 LYS B 25 71.11 62.40
REMARK 500 6 ILE B 46 111.03 -27.28
REMARK 500 7 TYR A 2 -57.58 -20.01
REMARK 500 7 GLU A 5 -66.13 -98.23
REMARK 500 7 GLU B 5 -160.77 -112.65
REMARK 500 7 LEU B 7 -59.59 -177.62
REMARK 500 7 GLU B 44 36.94 -77.79
REMARK 500 7 THR B 45 -49.11 -156.65
REMARK 500 7 ILE B 46 -136.55 43.69
REMARK 500 8 LEU A 3 66.61 -164.12
REMARK 500 8 ARG A 4 -7.65 -153.89
REMARK 500 8 LEU A 7 -51.95 -129.18
REMARK 500 8 GLU B 5 -76.88 -125.73
REMARK 500 8 LEU B 6 6.78 -68.02
REMARK 500 8 LEU B 7 -56.31 -127.49
REMARK 500
REMARK 500 THIS ENTRY HAS 98 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 TYR A 2 0.09 SIDE CHAIN
REMARK 500 1 TYR B 2 0.07 SIDE CHAIN
REMARK 500 1 TYR B 17 0.09 SIDE CHAIN
REMARK 500 2 TYR B 2 0.10 SIDE CHAIN
REMARK 500 3 TYR A 2 0.18 SIDE CHAIN
REMARK 500 3 TYR A 17 0.09 SIDE CHAIN
REMARK 500 3 TYR B 2 0.07 SIDE CHAIN
REMARK 500 4 TYR A 2 0.08 SIDE CHAIN
REMARK 500 4 TYR B 2 0.07 SIDE CHAIN
REMARK 500 4 TYR B 17 0.09 SIDE CHAIN
REMARK 500 5 TYR A 17 0.07 SIDE CHAIN
REMARK 500 6 TYR B 2 0.08 SIDE CHAIN
REMARK 500 7 TYR A 17 0.13 SIDE CHAIN
REMARK 500 8 TYR B 2 0.09 SIDE CHAIN
REMARK 500 9 TYR B 2 0.09 SIDE CHAIN
REMARK 500 10 TYR A 2 0.07 SIDE CHAIN
REMARK 500 10 TYR A 23 0.08 SIDE CHAIN
REMARK 500 11 TYR A 17 0.09 SIDE CHAIN
REMARK 500 12 TYR A 17 0.14 SIDE CHAIN
REMARK 500 12 TYR B 2 0.14 SIDE CHAIN
REMARK 500 13 TYR A 2 0.10 SIDE CHAIN
REMARK 500 13 TYR A 17 0.07 SIDE CHAIN
REMARK 500 13 ARG B 4 0.09 SIDE CHAIN
REMARK 500 13 TYR B 17 0.07 SIDE CHAIN
REMARK 500 14 TYR B 17 0.07 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 A 49
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH2 B 49
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1EC5 RELATED DB: PDB
REMARK 900 1EC5 IS THE CRYSTAL STRUCTURE OF DF1-DI-ZN(II) DERIVATIVE
REMARK 900 RELATED ID: 1JMB RELATED DB: PDB
REMARK 900 1JMB IS THE CRYSTAL STRUCTURE OF A DF1 MUTANT (L13A-DF1) IN THE DI-
REMARK 900 MN(II) FORM (S.G. C 2 2 21)
REMARK 900 RELATED ID: 1JM0 RELATED DB: PDB
REMARK 900 1JM0 IS A DIFFERENT CRYSTALLINE FORM (S. G. P212121) OF 1JMB
REMARK 900 RELATED ID: 1LT1 RELATED DB: PDB
REMARK 900 1LT1 IS THE CRYSTAL STRUCTURE OF L13G-DF1 IN THE DI-MN(II) FORM
DBREF 1NVO A 0 49 PDB 1NVO 1NVO 0 49
DBREF 1NVO B 0 49 PDB 1NVO 1NVO 0 49
SEQRES 1 A 50 ACE ASP TYR LEU ARG GLU LEU LEU LYS LEU GLU LEU GLN
SEQRES 2 A 50 LEU ILE LYS GLN TYR ARG GLU ALA LEU GLU TYR VAL LYS
SEQRES 3 A 50 LEU PRO VAL LEU ALA LYS ILE LEU GLU ASP GLU GLU LYS
SEQRES 4 A 50 HIS ILE GLU TRP LEU GLU THR ILE LEU GLY NH2
SEQRES 1 B 50 ACE ASP TYR LEU ARG GLU LEU LEU LYS LEU GLU LEU GLN
SEQRES 2 B 50 LEU ILE LYS GLN TYR ARG GLU ALA LEU GLU TYR VAL LYS
SEQRES 3 B 50 LEU PRO VAL LEU ALA LYS ILE LEU GLU ASP GLU GLU LYS
SEQRES 4 B 50 HIS ILE GLU TRP LEU GLU THR ILE LEU GLY NH2
HET ACE A 0 6
HET NH2 A 49 3
HET ACE B 0 6
HET NH2 B 49 3
HETNAM ACE ACETYL GROUP
HETNAM NH2 AMINO GROUP
FORMUL 1 ACE 2(C2 H4 O)
FORMUL 1 NH2 2(H2 N)
HELIX 1 1 LEU A 7 LYS A 25 1 19
HELIX 2 2 LEU A 26 GLU A 44 1 19
HELIX 3 3 ASP B 1 LEU B 7 1 7
HELIX 4 4 LEU B 7 TYR B 23 1 17
HELIX 5 5 LEU B 26 ILE B 46 1 21
LINK C ACE A 0 N ASP A 1 1555 1555 1.34
LINK C GLY A 48 N NH2 A 49 1555 1555 1.33
LINK C ACE B 0 N ASP B 1 1555 1555 1.34
LINK C GLY B 48 N NH2 B 49 1555 1555 1.33
SITE 1 AC3 1 GLY A 48
SITE 1 AC4 1 GLY B 48
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 23 2 Bytes