HEADER TRANSFERASE/PEPTIDE 13-AUG-13 4C1Q TITLE CRYSTAL STRUCTURE OF THE PRDM9 SET DOMAIN IN COMPLEX WITH H3K4ME2 AND TITLE 2 ADOHCY. COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE PRDM9; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: SET DOMAIN, RESIDUES 198-368; COMPND 5 SYNONYM: PRDM9, HYBRID STERILITY PROTEIN 1, MEIOSIS-INDUCED FACTOR COMPND 6 CONTAINING A PR/SET DOMAIN AND ZINC-FINGER MO PR DOMAIN ZINC FINGER COMPND 7 PROTEIN 9, PR DOMAIN-CONTAINING PROTEIN 9; COMPND 8 EC: 2.1.1.43; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: HISTONE H3.1; COMPND 12 CHAIN: C; COMPND 13 FRAGMENT: N-TERMINUS, RESIDUES 2-11; COMPND 14 SYNONYM: HISTONE H3, HISTONE H3/A, HISTONE H3/B, HISTONE H3/C, HISTON COMPND 15 HISTONE H3/F, HISTONE H3/H, HISTONE H3/I, HISTONE H3/J, HISTONE H3/K, COMPND 16 HISTONE H3/L; COMPND 17 ENGINEERED: YES; COMPND 18 OTHER_DETAILS: DOUBLE METHYLATION ON LYSINE 4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: STAR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPROEXHTB; 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 TRANSFERASE-PEPTIDE COMPLEX, HISTONE METHYLTRANSFERASE, SET DOMAIN KEYWDS 2 H3K4ME3 EXPDTA X-RAY DIFFRACTION AUTHOR N.MATHIOUDAKIS,S.CUSACK,J.KADLEC REVDAT 4 20-DEC-23 4C1Q 1 REMARK LINK REVDAT 3 09-OCT-19 4C1Q 1 REMARK LINK REVDAT 2 06-NOV-13 4C1Q 1 JRNL REVDAT 1 16-OCT-13 4C1Q 0 JRNL AUTH H.WU,N.MATHIOUDAKIS,B.DIAGOURAGA,A.DONG,L.DOMBROVSKI, JRNL AUTH 2 F.BAUDAT,S.CUSACK,B.DE MASSY,J.KADLEC JRNL TITL MOLECULAR BASIS FOR THE REGULATION OF THE H3K4 JRNL TITL 2 METHYLTRANSFERASE ACTIVITY OF PRDM9. JRNL REF CELL REP. V. 5 13 2013 JRNL REFN ESSN 2211-1247 JRNL PMID 24095733 JRNL DOI 10.1016/J.CELREP.2013.08.035 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.54 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 20355 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) : 0.208 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1098 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1464 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.17 REMARK 3 BIN R VALUE (WORKING SET) : 0.2970 REMARK 3 BIN FREE R VALUE SET COUNT : 82 REMARK 3 BIN FREE R VALUE : 0.3250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2745 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.71000 REMARK 3 B22 (A**2) : -2.32000 REMARK 3 B33 (A**2) : -3.40000 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): 0.274 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.221 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.186 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.231 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2856 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2514 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3881 ; 1.325 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5799 ; 0.777 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 339 ; 6.501 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 155 ;31.529 ;24.258 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 429 ;14.548 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;15.919 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 388 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3305 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 696 ; 0.002 ; 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 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 4 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 199 A 280 1 REMARK 3 1 B 199 B 280 1 REMARK 3 2 A 291 A 293 1 REMARK 3 2 B 291 B 293 1 REMARK 3 3 A 306 A 323 1 REMARK 3 3 B 306 B 323 1 REMARK 3 4 A 325 A 355 1 REMARK 3 4 B 325 B 355 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT THERMAL 1 A (A**2): 2065 ; 4.89 ; 0.50 REMARK 3 TIGHT THERMAL 1 B (A**2): 2065 ; 4.89 ; 0.50 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 ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4C1Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-AUG-13. REMARK 100 THE DEPOSITION ID IS D_1290058012. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.939 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21499 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.300 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.64400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: PDB ENTRY 3RAY REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M BIS-TRIS REMARK 280 PH 5.5 AND 25% W/V PEG3350, VAPOR DIFFUSION, TEMPERATURE 278K 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 27.86500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.80500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.09000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.80500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.86500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.09000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.5 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: 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 194 REMARK 465 LYS A 368 REMARK 465 GLY B 194 REMARK 465 ALA B 195 REMARK 465 GLY B 358 REMARK 465 ASP B 359 REMARK 465 GLU B 360 REMARK 465 TYR B 361 REMARK 465 GLY B 362 REMARK 465 GLN B 363 REMARK 465 GLU B 364 REMARK 465 LEU B 365 REMARK 465 GLY B 366 REMARK 465 ILE B 367 REMARK 465 LYS B 368 REMARK 465 ARG C 8 REMARK 465 LYS C 9 REMARK 465 TYR C 10 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O LYS B 297 NH2 ARG B 337 2.19 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 ASP A 200 -32.92 -37.59 REMARK 500 GLU A 263 -50.64 -124.16 REMARK 500 ARG A 299 54.67 71.53 REMARK 500 ASP B 200 -34.32 -39.68 REMARK 500 GLU B 263 -50.14 -122.06 REMARK 500 ASP B 283 155.36 -49.21 REMARK 500 ARG B 299 71.71 55.13 REMARK 500 ASN B 300 -7.19 92.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU B 284 GLU B 285 147.40 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 493 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 205 SG REMARK 620 2 CYS A 208 SG 121.4 REMARK 620 3 CYS A 216 SG 123.3 93.9 REMARK 620 4 HIS A 219 ND1 118.8 83.5 107.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 493 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 205 SG REMARK 620 2 CYS B 208 SG 113.9 REMARK 620 3 CYS B 216 SG 121.0 90.1 REMARK 620 4 HIS B 219 ND1 122.4 84.4 112.4 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 SAH A 394 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 493 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 493 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1358 DBREF 4C1Q A 198 368 UNP Q96EQ9 PRDM9_MOUSE 198 368 DBREF 4C1Q B 198 368 UNP Q96EQ9 PRDM9_MOUSE 198 368 DBREF 4C1Q C 1 10 UNP P68431 H31_HUMAN 2 11 SEQADV 4C1Q GLY A 194 UNP Q96EQ9 EXPRESSION TAG SEQADV 4C1Q ALA A 195 UNP Q96EQ9 EXPRESSION TAG SEQADV 4C1Q MET A 196 UNP Q96EQ9 EXPRESSION TAG SEQADV 4C1Q SER A 197 UNP Q96EQ9 EXPRESSION TAG SEQADV 4C1Q GLY B 194 UNP Q96EQ9 EXPRESSION TAG SEQADV 4C1Q ALA B 195 UNP Q96EQ9 EXPRESSION TAG SEQADV 4C1Q MET B 196 UNP Q96EQ9 EXPRESSION TAG SEQADV 4C1Q SER B 197 UNP Q96EQ9 EXPRESSION TAG SEQADV 4C1Q TYR C 10 UNP P68431 SER 11 CONFLICT SEQRES 1 A 175 GLY ALA MET SER GLN ASP ASP ASP TYR LEU TYR CYS GLU SEQRES 2 A 175 LYS CYS GLN ASN PHE PHE ILE ASP SER CYS PRO ASN HIS SEQRES 3 A 175 GLY PRO PRO LEU PHE VAL LYS ASP SER MET VAL ASP ARG SEQRES 4 A 175 GLY HIS PRO ASN HIS SER VAL LEU SER LEU PRO PRO GLY SEQRES 5 A 175 LEU ARG ILE SER PRO SER GLY ILE PRO GLU ALA GLY LEU SEQRES 6 A 175 GLY VAL TRP ASN GLU ALA SER ASP LEU PRO VAL GLY LEU SEQRES 7 A 175 HIS PHE GLY PRO TYR GLU GLY GLN ILE THR GLU ASP GLU SEQRES 8 A 175 GLU ALA ALA ASN SER GLY TYR SER TRP LEU ILE THR LYS SEQRES 9 A 175 GLY ARG ASN CYS TYR GLU TYR VAL ASP GLY GLN ASP GLU SEQRES 10 A 175 SER GLN ALA ASN TRP MET ARG TYR VAL ASN CYS ALA ARG SEQRES 11 A 175 ASP ASP GLU GLU GLN ASN LEU VAL ALA PHE GLN TYR HIS SEQRES 12 A 175 ARG LYS ILE PHE TYR ARG THR CYS ARG VAL ILE ARG PRO SEQRES 13 A 175 GLY CYS GLU LEU LEU VAL TRP TYR GLY ASP GLU TYR GLY SEQRES 14 A 175 GLN GLU LEU GLY ILE LYS SEQRES 1 B 175 GLY ALA MET SER GLN ASP ASP ASP TYR LEU TYR CYS GLU SEQRES 2 B 175 LYS CYS GLN ASN PHE PHE ILE ASP SER CYS PRO ASN HIS SEQRES 3 B 175 GLY PRO PRO LEU PHE VAL LYS ASP SER MET VAL ASP ARG SEQRES 4 B 175 GLY HIS PRO ASN HIS SER VAL LEU SER LEU PRO PRO GLY SEQRES 5 B 175 LEU ARG ILE SER PRO SER GLY ILE PRO GLU ALA GLY LEU SEQRES 6 B 175 GLY VAL TRP ASN GLU ALA SER ASP LEU PRO VAL GLY LEU SEQRES 7 B 175 HIS PHE GLY PRO TYR GLU GLY GLN ILE THR GLU ASP GLU SEQRES 8 B 175 GLU ALA ALA ASN SER GLY TYR SER TRP LEU ILE THR LYS SEQRES 9 B 175 GLY ARG ASN CYS TYR GLU TYR VAL ASP GLY GLN ASP GLU SEQRES 10 B 175 SER GLN ALA ASN TRP MET ARG TYR VAL ASN CYS ALA ARG SEQRES 11 B 175 ASP ASP GLU GLU GLN ASN LEU VAL ALA PHE GLN TYR HIS SEQRES 12 B 175 ARG LYS ILE PHE TYR ARG THR CYS ARG VAL ILE ARG PRO SEQRES 13 B 175 GLY CYS GLU LEU LEU VAL TRP TYR GLY ASP GLU TYR GLY SEQRES 14 B 175 GLN GLU LEU GLY ILE LYS SEQRES 1 C 10 ALA ARG THR MLY GLN THR ALA ARG LYS TYR MODRES 4C1Q MLY C 4 LYS N-DIMETHYL-LYSINE HET MLY C 4 11 HET SAH A 394 26 HET ZN A 493 1 HET ZN B 493 1 HET GOL B1358 6 HETNAM MLY N-DIMETHYL-LYSINE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MLY C8 H18 N2 O2 FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 ZN 2(ZN 2+) FORMUL 7 GOL C3 H8 O3 FORMUL 8 HOH *61(H2 O) HELIX 1 1 ALA A 195 ASP A 199 5 5 HELIX 2 2 ASN A 236 SER A 241 1 6 HELIX 3 3 GLU A 285 SER A 289 5 5 HELIX 4 4 ASN A 314 VAL A 319 5 6 HELIX 5 5 GLY A 358 LEU A 365 1 8 HELIX 6 6 ASN B 236 SER B 241 1 6 HELIX 7 7 GLU B 285 SER B 289 5 5 HELIX 8 8 ASN B 314 VAL B 319 5 6 SHEET 1 AA 2 LEU A 203 CYS A 205 0 SHEET 2 AA 2 ASN A 210 PHE A 212 -1 O ASN A 210 N CYS A 205 SHEET 1 AB 4 PHE A 224 VAL A 225 0 SHEET 2 AB 4 HIS A 272 PHE A 273 1 O HIS A 272 N VAL A 225 SHEET 3 AB 4 LYS A 338 THR A 343 -1 O TYR A 341 N PHE A 273 SHEET 4 AB 4 LEU A 330 TYR A 335 -1 O VAL A 331 N ARG A 342 SHEET 1 AC 2 LEU A 246 PRO A 250 0 SHEET 2 AC 2 LEU A 258 ASN A 262 -1 O GLY A 259 N SER A 249 SHEET 1 AD 4 GLN A 279 THR A 281 0 SHEET 2 AD 4 TYR A 302 ASP A 306 -1 O TYR A 304 N THR A 281 SHEET 3 AD 4 SER A 292 THR A 296 -1 O TRP A 293 N VAL A 305 SHEET 4 AD 4 THR C 3 MLY C 4 1 O MLY C 4 N LEU A 294 SHEET 1 AE 2 ASN A 320 CYS A 321 0 SHEET 2 AE 2 LEU A 354 VAL A 355 1 N VAL A 355 O ASN A 320 SHEET 1 BA 2 LEU B 203 CYS B 205 0 SHEET 2 BA 2 ASN B 210 PHE B 212 -1 O ASN B 210 N CYS B 205 SHEET 1 BB 6 PHE B 224 VAL B 225 0 SHEET 2 BB 6 HIS B 272 PHE B 273 1 O HIS B 272 N VAL B 225 SHEET 3 BB 6 LYS B 338 THR B 343 -1 O TYR B 341 N PHE B 273 SHEET 4 BB 6 LEU B 330 TYR B 335 -1 O VAL B 331 N ARG B 342 SHEET 5 BB 6 LEU B 354 TRP B 356 1 O LEU B 354 N LEU B 330 SHEET 6 BB 6 ASN B 320 CYS B 321 1 O ASN B 320 N VAL B 355 SHEET 1 BC 2 LEU B 246 PRO B 250 0 SHEET 2 BC 2 LEU B 258 ASN B 262 -1 O GLY B 259 N SER B 249 SHEET 1 BD 3 GLN B 279 THR B 281 0 SHEET 2 BD 3 TYR B 302 ASP B 306 -1 O TYR B 304 N THR B 281 SHEET 3 BD 3 SER B 292 THR B 296 -1 O TRP B 293 N VAL B 305 LINK C THR C 3 N MLY C 4 1555 1555 1.33 LINK C MLY C 4 N GLN C 5 1555 1555 1.33 LINK SG CYS A 205 ZN ZN A 493 1555 1555 2.16 LINK SG CYS A 208 ZN ZN A 493 1555 1555 2.17 LINK SG CYS A 216 ZN ZN A 493 1555 1555 2.33 LINK ND1 HIS A 219 ZN ZN A 493 1555 1555 2.47 LINK SG CYS B 205 ZN ZN B 493 1555 1555 2.20 LINK SG CYS B 208 ZN ZN B 493 1555 1555 2.26 LINK SG CYS B 216 ZN ZN B 493 1555 1555 2.34 LINK ND1 HIS B 219 ZN ZN B 493 1555 1555 2.28 CISPEP 1 GLY A 274 PRO A 275 0 9.47 CISPEP 2 GLY B 274 PRO B 275 0 10.84 SITE 1 AC1 14 ILE A 253 ALA A 256 LEU A 258 TYR A 291 SITE 2 AC1 14 ARG A 317 ASN A 320 CYS A 321 ARG A 323 SITE 3 AC1 14 TYR A 357 TYR A 361 HOH A2024 HOH A2035 SITE 4 AC1 14 ARG C 2 MLY C 4 SITE 1 AC2 4 CYS A 205 CYS A 208 CYS A 216 HIS A 219 SITE 1 AC3 4 CYS B 205 CYS B 208 CYS B 216 HIS B 219 SITE 1 AC4 5 TYR B 276 GLY B 290 SER B 292 TRP B 293 SITE 2 AC4 5 VAL B 319 CRYST1 55.730 78.180 107.610 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 0.017944 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012791 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009293 0.00000 MTRIX1 1 0.998392 0.034147 -0.045252 -12.65421 1 MTRIX2 1 -0.045571 0.008640 -0.998924 -18.50190 1 MTRIX3 1 -0.033719 0.999380 0.010182 20.34540 1