10 20 30 40 50 60 70 80 1J47 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric Unit
HEADER TRANSCRIPTION/DNA 23-JUL-01 1J47
TITLE 3D SOLUTION NMR STRUCTURE OF THE M9I MUTANT OF THE HMG-BOX TITLE 2 DOMAIN OF THE HUMAN MALE SEX DETERMINING FACTOR SRY TITLE 3 COMPLEXED TO DNA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: SEX-DETERMINING REGION Y PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HMG-BOX DOMAIN; COMPND 5 SYNONYM: SRY; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*CP*CP*TP*GP*CP*AP*CP*AP*AP*AP*CP*AP*CP*C)- COMPND 10 3'; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-D(*GP*GP*TP*GP*TP*TP*TP*GP*TP*GP*CP*AP*GP*G)- COMPND 15 3'; COMPND 16 CHAIN: C; COMPND 17 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET21A; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES
KEYWDS MALE SEX DETERMINING FACTOR, SRY, SEX-REVERSAL MUTATION, KEYWDS 2 DNA BENDING MUTANT, DIPOLAR COUPLINGS, MULTIDIMENSIONAL NMR, KEYWDS 3 TRANSCRIPTION/DNA COMPLEX
EXPDTA SOLUTION NMR
AUTHOR G.M.CLORE,E.C.MURPHY
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, JRNL AUTH 2 G.M.CLORE JRNL TITL STRUCTURAL BASIS FOR SRY-DEPENDENT 46-X,Y SEX JRNL TITL 2 REVERSAL: MODULATION OF DNA BENDING BY A NATURALLY JRNL TITL 3 OCCURRING POINT 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 1
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. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUL-01. REMARK 100 THE RCSB ID CODE IS RCSB001591.
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) DOUBLE REMARK 210 AND TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN; (2) DOUBLE REMARK 210 RESONANCE AND HETERONUCLEAR FILTERED FOR DNA; (3) QUANTITATIVE REMARK 210 J CORRELATION FOR COUPLING CONSTANTS; (4) 2D, 3D AND 4D REMARK 210 HETERONUCLEAR SEPARATED AND FILTERED NOE EXPERIMENTS; (4) 2D REMARK 210 AND 3D DOUBLE AND TRIPLE RESONANCE EXPERIMENTS FOR DIPOLAR REMARK 210 COUPLING MEASUREMENTS IN LIQUID CRYSTALLINE MEDIUM OF 4.5-5% REMARK 210 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 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. = -4.6 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 REMARK 900 FACTOR 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
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 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
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 1.000 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