PDB Short entry for 1J47 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 5 27-DEC-23 1J47 1 REMARK 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