HEADER GENE REGULATION/INHIBITOR 10-JAN-19 6NM4 TITLE CRYSTAL STRUCTURE OF SAM-BOUND PRDM9 IN COMPLEX WITH MRK-740 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE PRDM9; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PR-SET DOMAIN (UNP RESIDUES 195-385); COMPND 5 SYNONYM: PR DOMAIN ZINC FINGER PROTEIN 9, PR DOMAIN-CONTAINING COMPND 6 PROTEIN 9; COMPND 7 EC: 2.1.1.43; COMPND 8 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: PRDM9, PFM6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PR SET DOMAIN, LYSINE METHYLTRANSFERASE, INHIBITOR, STRUCTURAL KEYWDS 2 GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, GENE REGULATION- KEYWDS 3 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.IVANOCHKO,L.HALABELIAN,C.FISCHER,J.M.SANDERS,S.D.KATTAR,P.J.BROWN, AUTHOR 2 A.M.EDWARDS,C.BOUNTRA,C.H.ARROWSMITH,STRUCTURAL GENOMICS CONSORTIUM AUTHOR 3 (SGC) REVDAT 3 11-OCT-23 6NM4 1 REMARK REVDAT 2 25-DEC-19 6NM4 1 JRNL REVDAT 1 13-FEB-19 6NM4 0 JRNL AUTH A.ALLALI-HASSANI,M.M.SZEWCZYK,D.IVANOCHKO,S.L.ORGAN,J.BOK, JRNL AUTH 2 J.S.Y.HO,F.P.H.GAY,F.LI,L.BLAZER,M.S.ERAM,L.HALABELIAN, JRNL AUTH 3 D.DILWORTH,G.M.LUCIANI,E.LIMA-FERNANDES,Q.WU,P.LOPPNAU, JRNL AUTH 4 N.PALMER,S.Z.A.TALIB,P.J.BROWN,M.SCHAPIRA,P.KALDIS, JRNL AUTH 5 R.C.O'HAGAN,E.GUCCIONE,D.BARSYTE-LOVEJOY,C.H.ARROWSMITH, JRNL AUTH 6 J.M.SANDERS,S.D.KATTAR,D.J.BENNETT,B.NICHOLSON,M.VEDADI JRNL TITL DISCOVERY OF A CHEMICAL PROBE FOR PRDM9. JRNL REF NAT COMMUN V. 10 5759 2019 JRNL REFN ESSN 2041-1723 JRNL PMID 31848333 JRNL DOI 10.1038/S41467-019-13652-X REMARK 2 REMARK 2 RESOLUTION. 2.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0218 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 12587 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) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.258 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 664 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) : 2.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.65 REMARK 3 REFLECTION IN BIN (WORKING SET) : 904 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.3820 REMARK 3 BIN FREE R VALUE SET COUNT : 41 REMARK 3 BIN FREE R VALUE : 0.4720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2923 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 127 REMARK 3 SOLVENT ATOMS : 23 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.77000 REMARK 3 B22 (A**2) : -0.45000 REMARK 3 B33 (A**2) : -0.32000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.759 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.336 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.285 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 29.499 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.928 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3155 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2689 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4298 ; 1.537 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6238 ; 0.821 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 366 ; 6.900 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 155 ;33.365 ;24.065 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 455 ;17.198 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;12.308 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 416 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3724 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 688 ; 0.001 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 196 377 B 196 377 5587 0.100 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 195 A 402 REMARK 3 ORIGIN FOR THE GROUP (A): -1.8246 -20.5530 22.0176 REMARK 3 T TENSOR REMARK 3 T11: 0.2165 T22: 0.1512 REMARK 3 T33: 0.1071 T12: -0.0238 REMARK 3 T13: -0.0211 T23: 0.1149 REMARK 3 L TENSOR REMARK 3 L11: 2.2705 L22: 0.2182 REMARK 3 L33: 2.8707 L12: -0.3571 REMARK 3 L13: 1.2675 L23: -0.6454 REMARK 3 S TENSOR REMARK 3 S11: 0.3417 S12: -0.2784 S13: -0.1427 REMARK 3 S21: -0.1590 S22: -0.0369 S23: 0.0046 REMARK 3 S31: 0.3696 S32: -0.1835 S33: -0.3048 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 196 B 402 REMARK 3 ORIGIN FOR THE GROUP (A): -12.2956 9.4352 12.3379 REMARK 3 T TENSOR REMARK 3 T11: 0.1689 T22: 0.2070 REMARK 3 T33: 0.0730 T12: 0.0478 REMARK 3 T13: -0.0667 T23: -0.0976 REMARK 3 L TENSOR REMARK 3 L11: 0.4108 L22: 2.4334 REMARK 3 L33: 1.6356 L12: -0.3646 REMARK 3 L13: 0.2875 L23: 1.2461 REMARK 3 S TENSOR REMARK 3 S11: 0.0295 S12: -0.1808 S13: 0.0105 REMARK 3 S21: -0.4987 S22: 0.0805 S23: 0.0673 REMARK 3 S31: -0.1769 S32: 0.0286 S33: -0.1100 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : WITH TLS ADDED REMARK 4 REMARK 4 6NM4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-19. REMARK 100 THE DEPOSITION ID IS D_1000238962. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979180 REMARK 200 MONOCHROMATOR : CRYOGENICALLY-COOLED SINGLE REMARK 200 CRYSTAL SI(220) SIDE BOUNCE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.6.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13290 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.580 REMARK 200 RESOLUTION RANGE LOW (A) : 39.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.12900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.80 REMARK 200 R MERGE FOR SHELL (I) : 1.65500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 2.8.2 REMARK 200 STARTING MODEL: PDB ENTRY 4IJD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, PH 6.0, 0.2 M AMMONIUM REMARK 280 ACETATE, 24.5% PEG3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 19.01300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.71750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.40000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.71750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.01300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.40000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 380 REMARK 465 ARG A 381 REMARK 465 GLU A 382 REMARK 465 PRO A 383 REMARK 465 LYS A 384 REMARK 465 PRO A 385 REMARK 465 SER B 195 REMARK 465 ALA B 379 REMARK 465 GLY B 380 REMARK 465 ARG B 381 REMARK 465 GLU B 382 REMARK 465 PRO B 383 REMARK 465 LYS B 384 REMARK 465 PRO B 385 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 SER A 195 OG REMARK 470 LYS A 226 CD CE NZ REMARK 470 LYS A 232 CG CD CE NZ REMARK 470 ASP A 283 CG OD1 OD2 REMARK 470 GLU A 285 CG CD OE1 OE2 REMARK 470 ARG A 299 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 348 NE CZ NH1 NH2 REMARK 470 GLU B 196 CG CD OE1 OE2 REMARK 470 LYS B 226 CD CE NZ REMARK 470 GLU B 285 CG CD OE1 OE2 REMARK 470 GLU B 326 CG CD OE1 OE2 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 ASP A 214 CB - CG - OD1 ANGL. DEV. = 5.5 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 ILE A 213 -77.25 -96.08 REMARK 500 GLU A 263 -59.12 -130.56 REMARK 500 ALA A 264 -79.03 -41.43 REMARK 500 ILE B 213 -83.49 -97.72 REMARK 500 GLU B 263 -57.68 -127.28 REMARK 500 ALA B 264 -79.37 -47.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 205 SG REMARK 620 2 CYS A 208 SG 119.7 REMARK 620 3 CYS A 216 SG 113.8 89.1 REMARK 620 4 HIS A 219 ND1 110.7 105.3 116.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 205 SG REMARK 620 2 CYS B 208 SG 114.1 REMARK 620 3 CYS B 216 SG 123.4 94.9 REMARK 620 4 HIS B 219 ND1 104.5 96.5 120.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KS7 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SAM B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue KS7 B 403 DBREF 6NM4 A 195 385 UNP Q9NQV7 PRDM9_HUMAN 195 385 DBREF 6NM4 B 195 385 UNP Q9NQV7 PRDM9_HUMAN 195 385 SEQRES 1 A 191 SER GLU PRO GLN ASP ASP ASP TYR LEU TYR CYS GLU MET SEQRES 2 A 191 CYS GLN ASN PHE PHE ILE ASP SER CYS ALA ALA HIS GLY SEQRES 3 A 191 PRO PRO THR PHE VAL LYS ASP SER ALA VAL ASP LYS GLY SEQRES 4 A 191 HIS PRO ASN ARG SER ALA LEU SER LEU PRO PRO GLY LEU SEQRES 5 A 191 ARG ILE GLY PRO SER GLY ILE PRO GLN ALA GLY LEU GLY SEQRES 6 A 191 VAL TRP ASN GLU ALA SER ASP LEU PRO LEU GLY LEU HIS SEQRES 7 A 191 PHE GLY PRO TYR GLU GLY ARG ILE THR GLU ASP GLU GLU SEQRES 8 A 191 ALA ALA ASN ASN GLY TYR SER TRP LEU ILE THR LYS GLY SEQRES 9 A 191 ARG ASN CYS TYR GLU TYR VAL ASP GLY LYS ASP LYS SER SEQRES 10 A 191 TRP ALA ASN TRP MET ARG TYR VAL ASN CYS ALA ARG ASP SEQRES 11 A 191 ASP GLU GLU GLN ASN LEU VAL ALA PHE GLN TYR HIS ARG SEQRES 12 A 191 GLN ILE PHE TYR ARG THR CYS ARG VAL ILE ARG PRO GLY SEQRES 13 A 191 CYS GLU LEU LEU VAL TRP TYR GLY ASP GLU TYR GLY GLN SEQRES 14 A 191 GLU LEU GLY ILE LYS TRP GLY SER LYS TRP LYS LYS GLU SEQRES 15 A 191 LEU MET ALA GLY ARG GLU PRO LYS PRO SEQRES 1 B 191 SER GLU PRO GLN ASP ASP ASP TYR LEU TYR CYS GLU MET SEQRES 2 B 191 CYS GLN ASN PHE PHE ILE ASP SER CYS ALA ALA HIS GLY SEQRES 3 B 191 PRO PRO THR PHE VAL LYS ASP SER ALA VAL ASP LYS GLY SEQRES 4 B 191 HIS PRO ASN ARG SER ALA LEU SER LEU PRO PRO GLY LEU SEQRES 5 B 191 ARG ILE GLY PRO SER GLY ILE PRO GLN ALA GLY LEU GLY SEQRES 6 B 191 VAL TRP ASN GLU ALA SER ASP LEU PRO LEU GLY LEU HIS SEQRES 7 B 191 PHE GLY PRO TYR GLU GLY ARG ILE THR GLU ASP GLU GLU SEQRES 8 B 191 ALA ALA ASN ASN GLY TYR SER TRP LEU ILE THR LYS GLY SEQRES 9 B 191 ARG ASN CYS TYR GLU TYR VAL ASP GLY LYS ASP LYS SER SEQRES 10 B 191 TRP ALA ASN TRP MET ARG TYR VAL ASN CYS ALA ARG ASP SEQRES 11 B 191 ASP GLU GLU GLN ASN LEU VAL ALA PHE GLN TYR HIS ARG SEQRES 12 B 191 GLN ILE PHE TYR ARG THR CYS ARG VAL ILE ARG PRO GLY SEQRES 13 B 191 CYS GLU LEU LEU VAL TRP TYR GLY ASP GLU TYR GLY GLN SEQRES 14 B 191 GLU LEU GLY ILE LYS TRP GLY SER LYS TRP LYS LYS GLU SEQRES 15 B 191 LEU MET ALA GLY ARG GLU PRO LYS PRO HET ZN A 401 1 HET SAM A 402 27 HET KS7 A 403 34 HET UNX A 404 1 HET UNX A 405 1 HET ZN B 401 1 HET SAM B 402 27 HET KS7 B 403 34 HET UNX B 404 1 HETNAM ZN ZINC ION HETNAM SAM S-ADENOSYLMETHIONINE HETNAM KS7 4-[3-(3,5-DIMETHOXYPHENYL)-1,2,4-OXADIAZOL-5-YL]-1- HETNAM 2 KS7 METHYL-9-(2-METHYLPYRIDIN-4-YL)-1,4,9- HETNAM 3 KS7 TRIAZASPIRO[5.5]UNDECANE HETNAM UNX UNKNOWN ATOM OR ION FORMUL 3 ZN 2(ZN 2+) FORMUL 4 SAM 2(C15 H22 N6 O5 S) FORMUL 5 KS7 2(C25 H32 N6 O3) FORMUL 6 UNX 3(X) FORMUL 12 HOH *23(H2 O) HELIX 1 AA1 GLN A 198 TYR A 202 5 5 HELIX 2 AA2 ASN A 236 LEU A 242 1 7 HELIX 3 AA3 ASP A 283 ALA A 287 5 5 HELIX 4 AA4 ASN A 314 VAL A 319 5 6 HELIX 5 AA5 TYR A 361 LYS A 368 1 8 HELIX 6 AA6 LYS A 374 MET A 378 5 5 HELIX 7 AA7 GLN B 198 TYR B 202 5 5 HELIX 8 AA8 ASN B 236 LEU B 242 1 7 HELIX 9 AA9 ASP B 283 ALA B 287 5 5 HELIX 10 AB1 ASN B 314 VAL B 319 5 6 HELIX 11 AB2 TYR B 361 LYS B 368 1 8 HELIX 12 AB3 LYS B 374 MET B 378 5 5 SHEET 1 AA1 2 LEU A 203 CYS A 205 0 SHEET 2 AA1 2 ASN A 210 PHE A 212 -1 O ASN A 210 N CYS A 205 SHEET 1 AA2 7 THR A 223 VAL A 225 0 SHEET 2 AA2 7 LEU A 271 PHE A 273 1 O HIS A 272 N VAL A 225 SHEET 3 AA2 7 GLN A 338 THR A 343 -1 O TYR A 341 N PHE A 273 SHEET 4 AA2 7 LEU A 330 TYR A 335 -1 N TYR A 335 O GLN A 338 SHEET 5 AA2 7 GLU A 352 TYR A 357 1 O TRP A 356 N ALA A 332 SHEET 6 AA2 7 LEU A 258 ASN A 262 -1 N VAL A 260 O LEU A 353 SHEET 7 AA2 7 LEU A 246 PRO A 250 -1 N GLY A 249 O GLY A 259 SHEET 1 AA3 6 THR A 223 VAL A 225 0 SHEET 2 AA3 6 LEU A 271 PHE A 273 1 O HIS A 272 N VAL A 225 SHEET 3 AA3 6 GLN A 338 THR A 343 -1 O TYR A 341 N PHE A 273 SHEET 4 AA3 6 LEU A 330 TYR A 335 -1 N TYR A 335 O GLN A 338 SHEET 5 AA3 6 GLU A 352 TYR A 357 1 O TRP A 356 N ALA A 332 SHEET 6 AA3 6 ASN A 320 CYS A 321 1 N ASN A 320 O VAL A 355 SHEET 1 AA4 3 ARG A 279 THR A 281 0 SHEET 2 AA4 3 CYS A 301 ASP A 306 -1 O TYR A 304 N THR A 281 SHEET 3 AA4 3 SER A 292 GLY A 298 -1 N ILE A 295 O GLU A 303 SHEET 1 AA5 2 LEU B 203 CYS B 205 0 SHEET 2 AA5 2 ASN B 210 PHE B 212 -1 O ASN B 210 N CYS B 205 SHEET 1 AA6 7 PHE B 224 VAL B 225 0 SHEET 2 AA6 7 HIS B 272 PHE B 273 1 O HIS B 272 N VAL B 225 SHEET 3 AA6 7 GLN B 338 THR B 343 -1 O TYR B 341 N PHE B 273 SHEET 4 AA6 7 LEU B 330 TYR B 335 -1 N TYR B 335 O GLN B 338 SHEET 5 AA6 7 GLU B 352 TYR B 357 1 O TRP B 356 N ALA B 332 SHEET 6 AA6 7 LEU B 258 ASN B 262 -1 N VAL B 260 O LEU B 353 SHEET 7 AA6 7 LEU B 246 PRO B 250 -1 N GLY B 249 O GLY B 259 SHEET 1 AA7 6 PHE B 224 VAL B 225 0 SHEET 2 AA7 6 HIS B 272 PHE B 273 1 O HIS B 272 N VAL B 225 SHEET 3 AA7 6 GLN B 338 THR B 343 -1 O TYR B 341 N PHE B 273 SHEET 4 AA7 6 LEU B 330 TYR B 335 -1 N TYR B 335 O GLN B 338 SHEET 5 AA7 6 GLU B 352 TYR B 357 1 O TRP B 356 N ALA B 332 SHEET 6 AA7 6 ASN B 320 CYS B 321 1 N ASN B 320 O VAL B 355 SHEET 1 AA8 3 ARG B 279 THR B 281 0 SHEET 2 AA8 3 CYS B 301 ASP B 306 -1 O TYR B 304 N THR B 281 SHEET 3 AA8 3 SER B 292 GLY B 298 -1 N ILE B 295 O GLU B 303 LINK SG CYS A 205 ZN ZN A 401 1555 1555 2.27 LINK SG CYS A 208 ZN ZN A 401 1555 1555 2.32 LINK SG CYS A 216 ZN ZN A 401 1555 1555 2.33 LINK ND1 HIS A 219 ZN ZN A 401 1555 1555 2.10 LINK SG CYS B 205 ZN ZN B 401 1555 1555 2.31 LINK SG CYS B 208 ZN ZN B 401 1555 1555 2.32 LINK SG CYS B 216 ZN ZN B 401 1555 1555 2.34 LINK ND1 HIS B 219 ZN ZN B 401 1555 1555 2.27 CISPEP 1 GLY A 274 PRO A 275 0 9.98 CISPEP 2 GLY B 274 PRO B 275 0 10.40 SITE 1 AC1 4 CYS A 205 CYS A 208 CYS A 216 HIS A 219 SITE 1 AC2 10 ALA A 256 LEU A 258 GLY A 290 TYR A 291 SITE 2 AC2 10 ARG A 317 TYR A 318 VAL A 319 ASN A 320 SITE 3 AC2 10 CYS A 321 KS7 A 403 SITE 1 AC3 10 GLY A 290 SER A 292 TRP A 293 CYS A 321 SITE 2 AC3 10 ALA A 322 ASP A 324 TRP A 356 TYR A 361 SITE 3 AC3 10 SAM A 402 HOH A 507 SITE 1 AC4 4 CYS B 205 CYS B 208 CYS B 216 HIS B 219 SITE 1 AC5 11 ALA B 256 GLY B 257 LEU B 258 GLY B 290 SITE 2 AC5 11 TYR B 291 ARG B 317 TYR B 318 VAL B 319 SITE 3 AC5 11 ASN B 320 CYS B 321 KS7 B 403 SITE 1 AC6 13 ASP A 214 SER A 215 ALA A 217 ALA A 218 SITE 2 AC6 13 PRO A 221 GLY B 290 SER B 292 TRP B 293 SITE 3 AC6 13 ALA B 322 ASP B 324 ASP B 325 TRP B 356 SITE 4 AC6 13 SAM B 402 CRYST1 38.026 74.800 141.435 90.00 90.00 90.00 P 21 21 21 8 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 0.026298 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013369 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007070 0.00000