Header list of 1j47.pdb file
Complete list - 27 20 Bytes
HEADER TRANSCRIPTION/DNA 23-JUL-01 1J47
TITLE 3D SOLUTION NMR STRUCTURE OF THE M9I MUTANT OF THE HMG-BOX DOMAIN OF
TITLE 2 THE HUMAN MALE SEX DETERMINING FACTOR SRY COMPLEXED TO DNA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: 5'-D(*CP*CP*TP*GP*CP*AP*CP*AP*AP*AP*CP*AP*CP*C)-3';
COMPND 3 CHAIN: B;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: 5'-D(*GP*GP*TP*GP*TP*TP*TP*GP*TP*GP*CP*AP*GP*G)-3';
COMPND 7 CHAIN: C;
COMPND 8 ENGINEERED: YES;
COMPND 9 MOL_ID: 3;
COMPND 10 MOLECULE: SEX-DETERMINING REGION Y PROTEIN;
COMPND 11 CHAIN: A;
COMPND 12 FRAGMENT: HMG-BOX DOMAIN;
COMPND 13 SYNONYM: SRY;
COMPND 14 ENGINEERED: YES;
COMPND 15 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 SYNTHETIC: YES;
SOURCE 5 MOL_ID: 3;
SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 7 ORGANISM_COMMON: HUMAN;
SOURCE 8 ORGANISM_TAXID: 9606;
SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 10 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 11 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 12 EXPRESSION_SYSTEM_VECTOR: PET21A
KEYWDS MALE SEX DETERMINING FACTOR, SRY, SEX-REVERSAL MUTATION, DNA BENDING
KEYWDS 2 MUTANT, DIPOLAR COUPLINGS, MULTIDIMENSIONAL NMR, TRANSCRIPTION-DNA
KEYWDS 3 COMPLEX
EXPDTA SOLUTION NMR
AUTHOR G.M.CLORE,E.C.MURPHY
REVDAT 4 27-OCT-21 1J47 1 REMARK SEQADV
REVDAT 3 24-FEB-09 1J47 1 VERSN
REVDAT 2 01-APR-03 1J47 1 JRNL
REVDAT 1 03-OCT-01 1J47 0
JRNL AUTH E.C.MURPHY,V.B.ZHURKIN,J.M.LOUIS,G.CORNILESCU,G.M.CLORE
JRNL TITL STRUCTURAL BASIS FOR SRY-DEPENDENT 46-X,Y SEX REVERSAL:
JRNL TITL 2 MODULATION OF DNA BENDING BY A NATURALLY OCCURRING POINT
JRNL TITL 3 MUTATION.
JRNL REF J.MOL.BIOL. V. 312 481 2001
JRNL REFN ISSN 0022-2836
JRNL PMID 11563911
JRNL DOI 10.1006/JMBI.2001.4977
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : X-PLOR NIH VERSION (HTTP://NMR.CIT.NIH.GOV)
REMARK 3 (HTTP://NMR.CIT.NIH.GOV)
REMARK 3 AUTHORS : CLORE, KUSZEWSKI, SCHWIETERS
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE STRUCTURE WAS CALCULATED BY SIMULATED ANNEALING IN
REMARK 3 TORSION ANGLE SPACE (C. SCHWIETERS AND G.M. CLORE. J. MAGN.
REMARK 3 RESON., IN PRESS). THE TARGET FUNCTION COMPRISES TERMS FOR
REMARK 3 NOE RESTRAINTS, TORSION ANGLE RESTRAINTS, CARBON CHEMICAL
REMARK 3 SHIFT RESTRAINTS (KUSZWESKI ET AL. J. MAGN. RESON. SERIES B
REMARK 3 106, 92-96 (1995), J COUPLING RESTRAINTS (GARRETT ET AL. J.
REMARK 3 MAGN. RESON. SERIES B 104, 99, 103 (1994); DIPOLAR COUPLING
REMARK 3 RESTRAINTS (CLORE ET AL. J.MAGN.RESON. 131, 159-162 (1998);
REMARK 3 J.MAGN.RESON. 133, 216-221(1998)), AND RADIUS OF GYRATION
REMARK 3 (KUSZEWSKI ET AL. JACS 121, 2337 (1999)). THE NON-BONDED
REMARK 3 CONTACTS ARE REPRESENTED BY A QUARTIC VAN DER WAALS
REMARK 3 REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229,
REMARK 3 129-136); THE DELPHIC TORSION ANGLE DATABASE POTENTIAL
REMARK 3 (KUSZEWSKI & C J. MAGN. RESON. 146, 249 (2000)); AND THE
REMARK 3 DELPHIC BASE-BASE POSITIONAL DATABASE POTENTIAL (KUSZEWSKI
REMARK 3 ET AL. JACS 123, 3903 (2001)). IN THIS ENTRY THE SECOND TO
REMARK 3 LAST COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN
REMARK 3 THE INDIVIDUAL SIMULATED ANNEALING STRUCTURES (400 FOR THE
REMARK 3 WILD TYPE COMPLEX) AND THE MEAN COORDINATE POSITIONS
REMARK 3 (OBTAINED BY BEST FITTING TO RESIDUES 4-81 OF THE PROTEIN
REMARK 3 AND 101-128 OF THE DNA).
REMARK 3
REMARK 3 THE ORIENTATION PROVIDED FOR THE MUTANT (1J47) RELATIVE
REMARK 3 TO THE WILD TYPE (1J46) WAS OBTAINED BY BEST-FITTING TO
REMARK 3 RESIDUES 4-81 OF THE PROTEIN.
REMARK 3
REMARK 3 WILD TYPE M9I MUTANT
REMARK 3 PDB ID: 1J46 1J47
REMARK 3
REMARK 3 DEVIATIONS FROM IDEALIZED GEOMETRY:
REMARK 3 BONDS 0.003 A 0.003 A
REMARK 3 ANGLES 0.81 DEG 0.80 DEG
REMARK 3 IMPROPERS 0.79 DEG 0.79 DEG
REMARK 3
REMARK 3 DEVIATIONS FROM EXPT RESTRAINTS
REMARK 3 NOES (1795/1693) 0.04 A 0.03 A
REMARK 3 TORSION ANGLES (433/429) 0.29 DEG 0.30 DEG
REMARK 3 3JHNA COUPLINGS (70/66) 0.84 HZ 0.90 HZ
REMARK 3 13C CHEMICAL SHIFTS (165/165) 0.99 PPM 0.95 PPM
REMARK 3
REMARK 3 HETERONUCLEAR DIPOLAR COUPLING R-FACTORS
REMARK 3 (CLORE AND GARRETT J. AM. CHEM. SOC. 121, 9008-9012):
REMARK 3
REMARK 3 PROTEIN 1DNH (71/66) 5.5% 7.6%
REMARK 3 PROTEIN 1DCH (67/67) 6.3% 10.0%
REMARK 3 PROTEIN 1DNC' (68/62) 18.9% 28.9%
REMARK 3 PROTEIN 2DHNC'(68/62) 18.8% 21.6%
REMARK 3 DNA 1DNH (9/10) 10.2% 16.1%
REMARK 3 DNA 1DCH (37/33) 11.2% 10.7%
REMARK 3 DNA 1H-1H DIPOLAR
REMARK 3
REMARK 3 COUPLINGS (55/53) 0.56 HZ 0.75 HZ
REMARK 3 % RESIDUES IN MOST FAVORABLE
REMARK 3 REGION OF RAMACHADRAN MAP 94.7% 94.7%
REMARK 4
REMARK 4 1J47 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-01.
REMARK 100 THE DEPOSITION ID IS D_1000001591.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 308.00
REMARK 210 PH : 7.2
REMARK 210 IONIC STRENGTH : 50 MM SODIUM PHOSPHATE
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ
REMARK 210 SPECTROMETER MODEL : DMX500; DRX600; DRX750
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : NULL
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 400
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : RESTRAINED REGULARIZED MEAN
REMARK 210 STRUCTURE
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: THE FOLLOWING EXPERIMENTS WERE CONDUCTED: (1)
REMARK 210 DOUBLE AND TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN; (2)
REMARK 210 DOUBLE RESONANCE AND HETERONUCLEAR FILTERED FOR DNA; (3)
REMARK 210 QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS; (4) 2D,
REMARK 210 3D AND 4D HETERONUCLEAR SEPARATED AND FILTERED
REMARK 210 NOE EXPERIMENTS; (4) 2D AND 3D DOUBLE AND TRIPLE
REMARK 210 RESONANCE EXPERIMENTS FOR DIPOLAR COUPLING MEASUREMENTS
REMARK 210 IN LIQUID CRYSTALLINE MEDIUM OF 4.5-5% 3:1 DMPC:DHPC
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: TRIMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 HH12 ARG A 7 HH TYR A 74 1.24
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 DT B 103 C5 DT B 103 C7 0.037
REMARK 500 DT C 119 C5 DT C 119 C7 0.037
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 DT C 117 C6 - C5 - C7 ANGL. DEV. = -5.9 DEGREES
REMARK 500 DT C 119 C6 - C5 - C7 ANGL. DEV. = -4.4 DEGREES
REMARK 500 DT C 121 C6 - C5 - C7 ANGL. DEV. = -4.7 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 ALA A 80 93.48 -46.23
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1J46 RELATED DB: PDB
REMARK 900 WILD TYPE HMG-BOX DOMAIN OF THE HUMAN MALE SEX DETERMINING FACTOR
REMARK 900 SRY COMPLEXED TO DNA
DBREF 1J47 A 2 85 UNP Q05066 SRY_HUMAN 57 140
DBREF 1J47 B 101 114 PDB 1J47 1J47 101 114
DBREF 1J47 C 115 128 PDB 1J47 1J47 115 128
SEQADV 1J47 MET A 1 UNP Q05066 CLONING ARTIFACT
SEQADV 1J47 ILE A 9 UNP Q05066 MET 64 ENGINEERED MUTATION
SEQRES 1 B 14 DC DC DT DG DC DA DC DA DA DA DC DA DC
SEQRES 2 B 14 DC
SEQRES 1 C 14 DG DG DT DG DT DT DT DG DT DG DC DA DG
SEQRES 2 C 14 DG
SEQRES 1 A 85 MET GLN ASP ARG VAL LYS ARG PRO ILE ASN ALA PHE ILE
SEQRES 2 A 85 VAL TRP SER ARG ASP GLN ARG ARG LYS MET ALA LEU GLU
SEQRES 3 A 85 ASN PRO ARG MET ARG ASN SER GLU ILE SER LYS GLN LEU
SEQRES 4 A 85 GLY TYR GLN TRP LYS MET LEU THR GLU ALA GLU LYS TRP
SEQRES 5 A 85 PRO PHE PHE GLN GLU ALA GLN LYS LEU GLN ALA MET HIS
SEQRES 6 A 85 ARG GLU LYS TYR PRO ASN TYR LYS TYR ARG PRO ARG ARG
SEQRES 7 A 85 LYS ALA LYS MET LEU PRO LYS
HELIX 1 1 ASN A 10 ASN A 27 1 18
HELIX 2 2 ARG A 31 LYS A 44 1 14
HELIX 3 3 THR A 47 TYR A 69 1 23
CRYST1 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
Complete list - 27 20 Bytes