HEADER TRANSCRIPTION 10-FEB-12 4DOR TITLE HUMAN NUCLEAR RECEPTOR LIVER RECEPTOR HOMOLOGUE-1, LRH-1, IN ITS APO TITLE 2 STATE BOUND TO A FRAGMENT OF HUMAN SHP BOX1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR RECEPTOR SUBFAMILY 5 GROUP A MEMBER 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 290-541; COMPND 5 SYNONYM: ALPHA-1-FETOPROTEIN TRANSCRIPTION FACTOR, B1-BINDING FACTOR, COMPND 6 HB1F, CYP7A PROMOTER-BINDING FACTOR, HEPATOCYTIC TRANSCRIPTION COMPND 7 FACTOR, LIVER RECEPTOR HOMOLOG 1, LRH-1; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: NUCLEAR RECEPTOR SUBFAMILY 0 GROUP B MEMBER 2; COMPND 11 CHAIN: C, D; COMPND 12 FRAGMENT: UNP RESIDUES 15-28; COMPND 13 SYNONYM: ORPHAN NUCLEAR RECEPTOR SHP, SMALL HETERODIMER PARTNER; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: B1F, CPF, FTF, LRH-1, NR5A2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PLIC_MBP; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS NUCLEAR RECEPTOR, LIGAND BINDING DOMAIN, PHOSPHOLIPIDS, NR5A, KEYWDS 2 DIABETES, PHOSPHATIDYLCHOLINE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR P.M.MUSILLE,E.A.ORTLUND REVDAT 4 28-FEB-24 4DOR 1 REMARK SEQADV REVDAT 3 15-NOV-17 4DOR 1 REMARK REVDAT 2 16-MAY-12 4DOR 1 JRNL REVDAT 1 18-APR-12 4DOR 0 JRNL AUTH P.M.MUSILLE,M.C.PATHAK,J.L.LAUER,W.H.HUDSON,P.R.GRIFFIN, JRNL AUTH 2 E.A.ORTLUND JRNL TITL ANTIDIABETIC PHOSPHOLIPID-NUCLEAR RECEPTOR COMPLEX REVEALS JRNL TITL 2 THE MECHANISM FOR PHOSPHOLIPID-DRIVEN GENE REGULATION. JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 532 2012 JRNL REFN ISSN 1545-9993 JRNL PMID 22504882 JRNL DOI 10.1038/NSMB.2279 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0091 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 42702 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2149 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2749 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.1980 REMARK 3 BIN FREE R VALUE SET COUNT : 147 REMARK 3 BIN FREE R VALUE : 0.2430 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3882 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.49000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : 0.77000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.36000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.355 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.135 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.731 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4003 ; 0.014 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5393 ; 1.255 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 473 ; 4.621 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 194 ;40.363 ;25.258 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 744 ;13.515 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;23.734 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 608 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2956 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 11266 ; 4.293 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 165 ; 8.293 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3933 ; 6.071 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4DOR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070594. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42806 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9.5%-15% PEG 3350, 5% GLYCEROL, AND 50 REMARK 280 MM BIS-TRIS, PH 6.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 29.71950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 287 REMARK 465 GLU A 288 REMARK 465 PHE A 289 REMARK 465 MET A 290 REMARK 465 ASP A 291 REMARK 465 SER A 292 REMARK 465 TYR A 293 REMARK 465 GLN A 294 REMARK 465 THR A 295 REMARK 465 SER A 296 REMARK 465 SER A 297 REMARK 465 PRO A 298 REMARK 465 ALA A 299 REMARK 465 GLY A 398 REMARK 465 LYS A 399 REMARK 465 GLU A 400 REMARK 465 GLY A 401 REMARK 465 SER A 402 REMARK 465 ILE A 403 REMARK 465 PHE A 404 REMARK 465 LEU A 405 REMARK 465 VAL A 406 REMARK 465 THR A 407 REMARK 465 GLY A 408 REMARK 465 GLN A 409 REMARK 465 GLN A 410 REMARK 465 VAL A 411 REMARK 465 ASP A 412 REMARK 465 TYR A 413 REMARK 465 SER A 414 REMARK 465 ILE A 415 REMARK 465 ILE A 416 REMARK 465 ALA A 417 REMARK 465 SER A 418 REMARK 465 GLN A 419 REMARK 465 ALA A 420 REMARK 465 LYS A 539 REMARK 465 ARG A 540 REMARK 465 ALA A 541 REMARK 465 GLY B 287 REMARK 465 GLU B 288 REMARK 465 PHE B 289 REMARK 465 MET B 290 REMARK 465 ASP B 291 REMARK 465 SER B 292 REMARK 465 TYR B 293 REMARK 465 GLN B 294 REMARK 465 THR B 295 REMARK 465 SER B 296 REMARK 465 SER B 297 REMARK 465 PRO B 298 REMARK 465 ALA B 299 REMARK 465 ARG B 540 REMARK 465 ALA B 541 REMARK 465 ALA C 15 REMARK 465 SER C 28 REMARK 465 ALA D 15 REMARK 465 SER D 16 REMARK 465 ARG D 17 REMARK 465 SER D 28 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 462 CG CD CE NZ REMARK 470 SER C 16 N CB OG 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 ARG A 502 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 502 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG B 502 NE - CZ - NH1 ANGL. DEV. = 3.4 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 PHE A 365 -57.12 80.10 REMARK 500 ALA A 422 -57.12 -141.50 REMARK 500 ASN A 466 76.58 -110.01 REMARK 500 ASN B 466 65.61 -113.65 REMARK 500 TYR B 528 -162.35 -126.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 EPH B 601 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EPH B 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DOR RELATED DB: PDB DBREF 4DOR A 290 541 UNP O00482 NR5A2_HUMAN 290 541 DBREF 4DOR B 290 541 UNP O00482 NR5A2_HUMAN 290 541 DBREF 4DOR C 15 28 UNP Q15466 NR0B2_HUMAN 15 28 DBREF 4DOR D 15 28 UNP Q15466 NR0B2_HUMAN 15 28 SEQADV 4DOR GLY A 287 UNP O00482 EXPRESSION TAG SEQADV 4DOR GLU A 288 UNP O00482 EXPRESSION TAG SEQADV 4DOR PHE A 289 UNP O00482 EXPRESSION TAG SEQADV 4DOR GLY B 287 UNP O00482 EXPRESSION TAG SEQADV 4DOR GLU B 288 UNP O00482 EXPRESSION TAG SEQADV 4DOR PHE B 289 UNP O00482 EXPRESSION TAG SEQRES 1 A 255 GLY GLU PHE MET ASP SER TYR GLN THR SER SER PRO ALA SEQRES 2 A 255 SER ILE PRO HIS LEU ILE LEU GLU LEU LEU LYS CYS GLU SEQRES 3 A 255 PRO ASP GLU PRO GLN VAL GLN ALA LYS ILE MET ALA TYR SEQRES 4 A 255 LEU GLN GLN GLU GLN ALA ASN ARG SER LYS HIS GLU LYS SEQRES 5 A 255 LEU SER THR PHE GLY LEU MET CYS LYS MET ALA ASP GLN SEQRES 6 A 255 THR LEU PHE SER ILE VAL GLU TRP ALA ARG SER SER ILE SEQRES 7 A 255 PHE PHE ARG GLU LEU LYS VAL ASP ASP GLN MET LYS LEU SEQRES 8 A 255 LEU GLN ASN CYS TRP SER GLU LEU LEU ILE LEU ASP HIS SEQRES 9 A 255 ILE TYR ARG GLN VAL VAL HIS GLY LYS GLU GLY SER ILE SEQRES 10 A 255 PHE LEU VAL THR GLY GLN GLN VAL ASP TYR SER ILE ILE SEQRES 11 A 255 ALA SER GLN ALA GLY ALA THR LEU ASN ASN LEU MET SER SEQRES 12 A 255 HIS ALA GLN GLU LEU VAL ALA LYS LEU ARG SER LEU GLN SEQRES 13 A 255 PHE ASP GLN ARG GLU PHE VAL CYS LEU LYS PHE LEU VAL SEQRES 14 A 255 LEU PHE SER LEU ASP VAL LYS ASN LEU GLU ASN PHE GLN SEQRES 15 A 255 LEU VAL GLU GLY VAL GLN GLU GLN VAL ASN ALA ALA LEU SEQRES 16 A 255 LEU ASP TYR THR MET CYS ASN TYR PRO GLN GLN THR GLU SEQRES 17 A 255 LYS PHE GLY GLN LEU LEU LEU ARG LEU PRO GLU ILE ARG SEQRES 18 A 255 ALA ILE SER MET GLN ALA GLU GLU TYR LEU TYR TYR LYS SEQRES 19 A 255 HIS LEU ASN GLY ASP VAL PRO TYR ASN ASN LEU LEU ILE SEQRES 20 A 255 GLU MET LEU HIS ALA LYS ARG ALA SEQRES 1 B 255 GLY GLU PHE MET ASP SER TYR GLN THR SER SER PRO ALA SEQRES 2 B 255 SER ILE PRO HIS LEU ILE LEU GLU LEU LEU LYS CYS GLU SEQRES 3 B 255 PRO ASP GLU PRO GLN VAL GLN ALA LYS ILE MET ALA TYR SEQRES 4 B 255 LEU GLN GLN GLU GLN ALA ASN ARG SER LYS HIS GLU LYS SEQRES 5 B 255 LEU SER THR PHE GLY LEU MET CYS LYS MET ALA ASP GLN SEQRES 6 B 255 THR LEU PHE SER ILE VAL GLU TRP ALA ARG SER SER ILE SEQRES 7 B 255 PHE PHE ARG GLU LEU LYS VAL ASP ASP GLN MET LYS LEU SEQRES 8 B 255 LEU GLN ASN CYS TRP SER GLU LEU LEU ILE LEU ASP HIS SEQRES 9 B 255 ILE TYR ARG GLN VAL VAL HIS GLY LYS GLU GLY SER ILE SEQRES 10 B 255 PHE LEU VAL THR GLY GLN GLN VAL ASP TYR SER ILE ILE SEQRES 11 B 255 ALA SER GLN ALA GLY ALA THR LEU ASN ASN LEU MET SER SEQRES 12 B 255 HIS ALA GLN GLU LEU VAL ALA LYS LEU ARG SER LEU GLN SEQRES 13 B 255 PHE ASP GLN ARG GLU PHE VAL CYS LEU LYS PHE LEU VAL SEQRES 14 B 255 LEU PHE SER LEU ASP VAL LYS ASN LEU GLU ASN PHE GLN SEQRES 15 B 255 LEU VAL GLU GLY VAL GLN GLU GLN VAL ASN ALA ALA LEU SEQRES 16 B 255 LEU ASP TYR THR MET CYS ASN TYR PRO GLN GLN THR GLU SEQRES 17 B 255 LYS PHE GLY GLN LEU LEU LEU ARG LEU PRO GLU ILE ARG SEQRES 18 B 255 ALA ILE SER MET GLN ALA GLU GLU TYR LEU TYR TYR LYS SEQRES 19 B 255 HIS LEU ASN GLY ASP VAL PRO TYR ASN ASN LEU LEU ILE SEQRES 20 B 255 GLU MET LEU HIS ALA LYS ARG ALA SEQRES 1 C 14 ALA SER ARG PRO ALA ILE LEU TYR ALA LEU LEU SER SER SEQRES 2 C 14 SER SEQRES 1 D 14 ALA SER ARG PRO ALA ILE LEU TYR ALA LEU LEU SER SER SEQRES 2 D 14 SER HET EPH B 601 47 HETNAM EPH L-ALPHA-PHOSPHATIDYL-BETA-OLEOYL-GAMMA-PALMITOYL- HETNAM 2 EPH PHOSPHATIDYLETHANOLAMINE FORMUL 5 EPH C39 H68 N O8 P FORMUL 6 HOH *165(H2 O) HELIX 1 1 PRO A 302 LYS A 310 1 9 HELIX 2 2 ASP A 314 ARG A 333 1 20 HELIX 3 3 SER A 340 SER A 363 1 24 HELIX 4 4 PHE A 365 LEU A 369 5 5 HELIX 5 5 LYS A 370 HIS A 397 1 28 HELIX 6 6 ALA A 422 GLN A 442 1 21 HELIX 7 7 ASP A 444 PHE A 457 1 14 HELIX 8 8 ASN A 466 TYR A 489 1 24 HELIX 9 9 GLU A 494 LEU A 501 1 8 HELIX 10 10 LEU A 501 ASN A 523 1 23 HELIX 11 11 ASN A 530 ALA A 538 1 9 HELIX 12 12 PRO B 302 LYS B 310 1 9 HELIX 13 13 ASP B 314 ASN B 332 1 19 HELIX 14 14 SER B 340 SER B 362 1 23 HELIX 15 15 SER B 363 GLU B 368 1 6 HELIX 16 16 LYS B 370 GLY B 398 1 29 HELIX 17 17 TYR B 413 ALA B 420 1 8 HELIX 18 18 GLY B 421 LEU B 441 1 21 HELIX 19 19 ASP B 444 PHE B 457 1 14 HELIX 20 20 ASN B 466 TYR B 489 1 24 HELIX 21 21 GLU B 494 LEU B 501 1 8 HELIX 22 22 LEU B 501 ASN B 523 1 23 HELIX 23 23 ASN B 530 HIS B 537 1 8 HELIX 24 24 PRO C 18 SER C 27 1 10 HELIX 25 25 ALA D 19 SER D 27 1 9 SHEET 1 A 2 SER B 402 PHE B 404 0 SHEET 2 A 2 GLN B 410 ASP B 412 -1 O VAL B 411 N ILE B 403 SITE 1 AC1 19 HIS A 336 GLU A 337 PHE B 342 TRP B 382 SITE 2 AC1 19 SER B 383 LEU B 386 ILE B 387 ILE B 416 SITE 3 AC1 19 ALA B 420 GLY B 421 LEU B 424 LEU B 427 SITE 4 AC1 19 MET B 428 ALA B 431 ILE B 509 GLU B 514 SITE 5 AC1 19 TYR B 516 LYS B 520 HOH B 716 CRYST1 63.522 59.439 74.201 90.00 100.13 90.00 P 1 21 1 4 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 0.015743 0.000000 0.002811 0.00000 SCALE2 0.000000 0.016824 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013690 0.00000