HEADER TRANSFERASE 21-DEC-12 4IJD TITLE CRYSTAL STRUCTURE OF METHYLTRANSFERASE DOMAIN OF HUMAN PR DOMAIN- TITLE 2 CONTAINING PROTEIN 9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE PRDM9; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 195-415; 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: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28-MHL KEYWDS PRDM9, METHYLTRANSFERASE, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM, SGC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.DONG,L.DOMBROVSKI,Y.LI,W.TEMPEL,C.BOUNTRA,C.H.ARROWSMITH, AUTHOR 2 A.M.EDWARDS,P.J.BROWN,H.WU,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 2 15-NOV-17 4IJD 1 REMARK REVDAT 1 13-FEB-13 4IJD 0 JRNL AUTH L.DOMBROVSKI,A.DONG,Y.LI,W.TEMPEL,C.BOUNTRA,C.H.ARROWSMITH, JRNL AUTH 2 A.M.EDWARDS,P.J.BROWN,H.WU, JRNL AUTH 3 STRUCTURAL GENOMICS CONSORTIUM (SGC) JRNL TITL CRYSTAL STRUCTURE OF METHYLTRANSFERASE DOMAIN OF HUMAN PR JRNL TITL 2 DOMAIN-CONTAINING PROTEIN 9 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.19 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 21794 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) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.200 REMARK 3 FREE R VALUE TEST SET COUNT : 911 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) : 2.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 951 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 60.54 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 40 REMARK 3 BIN FREE R VALUE : 0.3370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3275 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 59 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : 0.56000 REMARK 3 B33 (A**2) : -1.13000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.35000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.290 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.233 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.164 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.123 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3413 ; 0.011 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2913 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4650 ; 1.195 ; 1.939 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6668 ; 0.719 ; 3.004 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 431 ; 6.840 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 158 ;32.447 ;23.734 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 435 ;13.188 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;13.537 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 467 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4000 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 839 ; 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 NUMBER OF DIFFERENT NCS GROUPS : NULL 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 : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 195 A 413 REMARK 3 RESIDUE RANGE : A 501 A 502 REMARK 3 ORIGIN FOR THE GROUP (A): 10.2363 -0.4864 0.3803 REMARK 3 T TENSOR REMARK 3 T11: 0.0342 T22: 0.0332 REMARK 3 T33: 0.0631 T12: -0.0061 REMARK 3 T13: -0.0162 T23: -0.0212 REMARK 3 L TENSOR REMARK 3 L11: 3.8416 L22: 3.2820 REMARK 3 L33: 0.9260 L12: -2.2825 REMARK 3 L13: 0.0946 L23: -0.3316 REMARK 3 S TENSOR REMARK 3 S11: -0.0964 S12: -0.1070 S13: 0.1347 REMARK 3 S21: 0.1125 S22: 0.0702 S23: -0.1115 REMARK 3 S31: -0.1320 S32: -0.0408 S33: 0.0262 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 195 B 411 REMARK 3 RESIDUE RANGE : B 501 B 502 REMARK 3 ORIGIN FOR THE GROUP (A): 30.5330 -5.6112 36.1270 REMARK 3 T TENSOR REMARK 3 T11: 0.1930 T22: 0.1962 REMARK 3 T33: 0.1053 T12: 0.0643 REMARK 3 T13: 0.0475 T23: 0.0246 REMARK 3 L TENSOR REMARK 3 L11: 2.4132 L22: 3.5819 REMARK 3 L33: 1.3689 L12: 0.6363 REMARK 3 L13: -0.5177 L23: -0.7734 REMARK 3 S TENSOR REMARK 3 S11: 0.0458 S12: 0.0920 S13: 0.1114 REMARK 3 S21: -0.1552 S22: -0.0912 S23: -0.1592 REMARK 3 S31: 0.0791 S32: 0.0747 S33: 0.0454 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 : WITH TLS ADDED REMARK 4 REMARK 4 4IJD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000076825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-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 : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97912 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : S REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21804 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.09300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.80400 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: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% PEG 3350, 0.2 M AMMONIUM ACETATE, REMARK 280 0.1 M BISTRIS PH5.5, VAPOR DIFFUSION HANGING DROP, TEMPERATURE REMARK 280 291K, VAPOR DIFFUSION, HANGING DROP 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 24.39100 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 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 ALA A 379 REMARK 465 GLY A 380 REMARK 465 ARG A 381 REMARK 465 GLU A 382 REMARK 465 GLN A 414 REMARK 465 ASN A 415 REMARK 465 ALA B 379 REMARK 465 GLY B 380 REMARK 465 SER B 412 REMARK 465 SER B 413 REMARK 465 GLN B 414 REMARK 465 ASN B 415 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 ASP A 214 CG OD1 OD2 REMARK 470 LYS A 226 CG CD CE NZ REMARK 470 ASP A 231 CG OD1 OD2 REMARK 470 LYS A 232 CG CD CE NZ REMARK 470 HIS A 234 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A 279 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 284 CG CD OE1 OE2 REMARK 470 GLU A 285 CG CD OE1 OE2 REMARK 470 ASN A 288 CG OD1 ND2 REMARK 470 GLU A 303 CG CD OE1 OE2 REMARK 470 LYS A 308 CG CD CE NZ REMARK 470 SER A 311 OG REMARK 470 ARG A 348 CD NE CZ NH1 NH2 REMARK 470 GLN A 363 CG CD OE1 NE2 REMARK 470 GLU A 364 CD OE1 OE2 REMARK 470 ILE A 367 CG1 CG2 CD1 REMARK 470 LYS A 372 CG CD CE NZ REMARK 470 GLU A 376 CG CD OE1 OE2 REMARK 470 LYS A 384 CG CD CE NZ REMARK 470 ILE A 387 CG1 CD1 REMARK 470 GLN A 400 CD OE1 NE2 REMARK 470 LYS A 401 CD CE NZ REMARK 470 ARG A 409 CD NE CZ NH1 NH2 REMARK 470 SER B 195 OG REMARK 470 ASP B 214 CG OD1 OD2 REMARK 470 LYS B 226 CG CD CE NZ REMARK 470 ASP B 231 CG OD1 OD2 REMARK 470 LYS B 232 CG CD CE NZ REMARK 470 ILE B 253 CG1 CD1 REMARK 470 GLN B 255 CG CD OE1 NE2 REMARK 470 GLU B 263 CD OE1 OE2 REMARK 470 ILE B 280 CG1 CG2 CD1 REMARK 470 GLU B 284 CG CD OE1 OE2 REMARK 470 GLU B 285 CG CD OE1 OE2 REMARK 470 LYS B 297 CE NZ REMARK 470 LYS B 308 CG CD CE NZ REMARK 470 LYS B 310 CE NZ REMARK 470 ARG B 348 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 363 CG CD OE1 NE2 REMARK 470 GLU B 364 CD OE1 OE2 REMARK 470 ILE B 367 CG1 CG2 CD1 REMARK 470 LYS B 372 CG CD CE NZ REMARK 470 GLU B 376 CG CD OE1 OE2 REMARK 470 LEU B 377 CG CD1 CD2 REMARK 470 ARG B 381 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 384 CG CD CE NZ REMARK 470 GLU B 386 CG CD OE1 OE2 REMARK 470 LYS B 401 CG CD CE NZ REMARK 470 GLU B 408 CG CD OE1 OE2 REMARK 470 ARG B 409 CG CD NE CZ NH1 NH2 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 NH1 ARG A 345 O HOH A 618 2.18 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 TRP A 356 CE2 TRP A 356 CD2 0.073 REMARK 500 HIS B 411 CG HIS B 411 CD2 0.055 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 214 -66.14 81.76 REMARK 500 GLN A 255 -3.03 79.93 REMARK 500 GLU A 263 -54.62 -123.20 REMARK 500 ASN A 288 41.83 35.81 REMARK 500 HIS A 411 -41.84 -139.50 REMARK 500 SER A 412 118.77 -165.07 REMARK 500 GLU B 196 124.02 -171.76 REMARK 500 ASP B 214 -65.17 73.33 REMARK 500 GLU B 263 -60.29 -132.92 REMARK 500 ASN B 288 13.22 56.21 REMARK 500 ASN B 300 28.82 45.50 REMARK 500 ASN B 410 29.39 -158.14 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 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 406 NE2 REMARK 620 2 HIS A 411 NE2 100.9 REMARK 620 3 CYS A 393 SG 111.2 117.7 REMARK 620 4 CYS A 390 SG 98.8 102.4 122.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 406 NE2 REMARK 620 2 HIS B 411 NE2 104.3 REMARK 620 3 CYS B 390 SG 109.4 105.8 REMARK 620 4 CYS B 393 SG 102.4 116.0 118.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 219 ND1 REMARK 620 2 CYS B 205 SG 104.9 REMARK 620 3 CYS B 216 SG 120.9 125.1 REMARK 620 4 CYS B 208 SG 101.8 113.9 86.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 219 ND1 REMARK 620 2 CYS A 205 SG 105.8 REMARK 620 3 CYS A 216 SG 111.6 121.8 REMARK 620 4 CYS A 208 SG 97.7 114.6 102.9 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 502 DBREF 4IJD A 195 415 UNP Q9NQV7 PRDM9_HUMAN 195 415 DBREF 4IJD B 195 415 UNP Q9NQV7 PRDM9_HUMAN 195 415 SEQRES 1 A 221 SER GLU PRO GLN ASP ASP ASP TYR LEU TYR CYS GLU MSE SEQRES 2 A 221 CYS GLN ASN PHE PHE ILE ASP SER CYS ALA ALA HIS GLY SEQRES 3 A 221 PRO PRO THR PHE VAL LYS ASP SER ALA VAL ASP LYS GLY SEQRES 4 A 221 HIS PRO ASN ARG SER ALA LEU SER LEU PRO PRO GLY LEU SEQRES 5 A 221 ARG ILE GLY PRO SER GLY ILE PRO GLN ALA GLY LEU GLY SEQRES 6 A 221 VAL TRP ASN GLU ALA SER ASP LEU PRO LEU GLY LEU HIS SEQRES 7 A 221 PHE GLY PRO TYR GLU GLY ARG ILE THR GLU ASP GLU GLU SEQRES 8 A 221 ALA ALA ASN ASN GLY TYR SER TRP LEU ILE THR LYS GLY SEQRES 9 A 221 ARG ASN CYS TYR GLU TYR VAL ASP GLY LYS ASP LYS SER SEQRES 10 A 221 TRP ALA ASN TRP MSE ARG TYR VAL ASN CYS ALA ARG ASP SEQRES 11 A 221 ASP GLU GLU GLN ASN LEU VAL ALA PHE GLN TYR HIS ARG SEQRES 12 A 221 GLN ILE PHE TYR ARG THR CYS ARG VAL ILE ARG PRO GLY SEQRES 13 A 221 CYS GLU LEU LEU VAL TRP TYR GLY ASP GLU TYR GLY GLN SEQRES 14 A 221 GLU LEU GLY ILE LYS TRP GLY SER LYS TRP LYS LYS GLU SEQRES 15 A 221 LEU MSE ALA GLY ARG GLU PRO LYS PRO GLU ILE HIS PRO SEQRES 16 A 221 CYS PRO SER CYS CYS LEU ALA PHE SER SER GLN LYS PHE SEQRES 17 A 221 LEU SER GLN HIS VAL GLU ARG ASN HIS SER SER GLN ASN SEQRES 1 B 221 SER GLU PRO GLN ASP ASP ASP TYR LEU TYR CYS GLU MSE SEQRES 2 B 221 CYS GLN ASN PHE PHE ILE ASP SER CYS ALA ALA HIS GLY SEQRES 3 B 221 PRO PRO THR PHE VAL LYS ASP SER ALA VAL ASP LYS GLY SEQRES 4 B 221 HIS PRO ASN ARG SER ALA LEU SER LEU PRO PRO GLY LEU SEQRES 5 B 221 ARG ILE GLY PRO SER GLY ILE PRO GLN ALA GLY LEU GLY SEQRES 6 B 221 VAL TRP ASN GLU ALA SER ASP LEU PRO LEU GLY LEU HIS SEQRES 7 B 221 PHE GLY PRO TYR GLU GLY ARG ILE THR GLU ASP GLU GLU SEQRES 8 B 221 ALA ALA ASN ASN GLY TYR SER TRP LEU ILE THR LYS GLY SEQRES 9 B 221 ARG ASN CYS TYR GLU TYR VAL ASP GLY LYS ASP LYS SER SEQRES 10 B 221 TRP ALA ASN TRP MSE ARG TYR VAL ASN CYS ALA ARG ASP SEQRES 11 B 221 ASP GLU GLU GLN ASN LEU VAL ALA PHE GLN TYR HIS ARG SEQRES 12 B 221 GLN ILE PHE TYR ARG THR CYS ARG VAL ILE ARG PRO GLY SEQRES 13 B 221 CYS GLU LEU LEU VAL TRP TYR GLY ASP GLU TYR GLY GLN SEQRES 14 B 221 GLU LEU GLY ILE LYS TRP GLY SER LYS TRP LYS LYS GLU SEQRES 15 B 221 LEU MSE ALA GLY ARG GLU PRO LYS PRO GLU ILE HIS PRO SEQRES 16 B 221 CYS PRO SER CYS CYS LEU ALA PHE SER SER GLN LYS PHE SEQRES 17 B 221 LEU SER GLN HIS VAL GLU ARG ASN HIS SER SER GLN ASN MODRES 4IJD MSE A 207 MET SELENOMETHIONINE MODRES 4IJD MSE A 316 MET SELENOMETHIONINE MODRES 4IJD MSE A 378 MET SELENOMETHIONINE MODRES 4IJD MSE B 207 MET SELENOMETHIONINE MODRES 4IJD MSE B 316 MET SELENOMETHIONINE MODRES 4IJD MSE B 378 MET SELENOMETHIONINE HET MSE A 207 8 HET MSE A 316 8 HET MSE A 378 8 HET MSE B 207 8 HET MSE B 316 8 HET MSE B 378 8 HET ZN A 501 1 HET ZN A 502 1 HET UNX A 503 1 HET UNX A 504 1 HET UNX A 505 1 HET UNX A 506 1 HET UNX A 507 1 HET UNX A 508 1 HET UNX A 509 1 HET UNX A 510 1 HET UNX A 511 1 HET UNX A 512 1 HET UNX A 513 1 HET UNX A 514 1 HET UNX A 515 1 HET UNX A 516 1 HET UNX A 517 1 HET UNX A 518 1 HET ZN B 501 1 HET ZN B 502 1 HET UNX B 503 1 HET UNX B 504 1 HET UNX B 505 1 HET UNX B 506 1 HET UNX B 507 1 HET UNX B 508 1 HET UNX B 509 1 HET UNX B 510 1 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM UNX UNKNOWN ATOM OR ION FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 3 ZN 4(ZN 2+) FORMUL 5 UNX 24(X) FORMUL 31 HOH *59(H2 O) HELIX 1 1 GLN A 198 TYR A 202 5 5 HELIX 2 2 ASN A 236 SER A 241 1 6 HELIX 3 3 ASP A 283 ALA A 287 5 5 HELIX 4 4 ASN A 314 VAL A 319 5 6 HELIX 5 5 TYR A 361 LYS A 368 1 8 HELIX 6 6 LYS A 372 MSE A 378 1 7 HELIX 7 7 SER A 399 HIS A 411 1 13 HELIX 8 8 GLN B 198 TYR B 202 5 5 HELIX 9 9 ASN B 236 LEU B 242 1 7 HELIX 10 10 ASP B 283 ALA B 287 5 5 HELIX 11 11 ASP B 309 ALA B 313 5 5 HELIX 12 12 ASN B 314 VAL B 319 5 6 HELIX 13 13 TYR B 361 LYS B 368 1 8 HELIX 14 14 LYS B 372 MSE B 378 1 7 HELIX 15 15 SER B 399 HIS B 411 1 13 SHEET 1 A 2 LEU A 203 CYS A 205 0 SHEET 2 A 2 ASN A 210 PHE A 212 -1 O ASN A 210 N CYS A 205 SHEET 1 B 6 PHE A 224 VAL A 225 0 SHEET 2 B 6 HIS A 272 PHE A 273 1 O HIS A 272 N VAL A 225 SHEET 3 B 6 GLN A 338 THR A 343 -1 O TYR A 341 N PHE A 273 SHEET 4 B 6 LEU A 330 TYR A 335 -1 N TYR A 335 O GLN A 338 SHEET 5 B 6 LEU A 354 TRP A 356 1 O TRP A 356 N ALA A 332 SHEET 6 B 6 ASN A 320 CYS A 321 1 N ASN A 320 O VAL A 355 SHEET 1 C 2 LEU A 246 PRO A 250 0 SHEET 2 C 2 LEU A 258 ASN A 262 -1 O TRP A 261 N ARG A 247 SHEET 1 D 3 ARG A 279 THR A 281 0 SHEET 2 D 3 CYS A 301 ASP A 306 -1 O ASP A 306 N ARG A 279 SHEET 3 D 3 SER A 292 GLY A 298 -1 N ILE A 295 O GLU A 303 SHEET 1 E 2 HIS A 388 PRO A 389 0 SHEET 2 E 2 ALA A 396 PHE A 397 -1 O PHE A 397 N HIS A 388 SHEET 1 F 2 LEU B 203 CYS B 205 0 SHEET 2 F 2 ASN B 210 PHE B 212 -1 O ASN B 210 N CYS B 205 SHEET 1 G 6 PHE B 224 VAL B 225 0 SHEET 2 G 6 HIS B 272 PHE B 273 1 O HIS B 272 N VAL B 225 SHEET 3 G 6 GLN B 338 THR B 343 -1 O TYR B 341 N PHE B 273 SHEET 4 G 6 LEU B 330 TYR B 335 -1 N TYR B 335 O GLN B 338 SHEET 5 G 6 LEU B 354 TRP B 356 1 O TRP B 356 N ALA B 332 SHEET 6 G 6 ASN B 320 CYS B 321 1 N ASN B 320 O VAL B 355 SHEET 1 H 2 LEU B 246 PRO B 250 0 SHEET 2 H 2 LEU B 258 ASN B 262 -1 O TRP B 261 N ARG B 247 SHEET 1 I 3 ARG B 279 THR B 281 0 SHEET 2 I 3 TYR B 302 ASP B 306 -1 O TYR B 304 N THR B 281 SHEET 3 I 3 SER B 292 THR B 296 -1 N ILE B 295 O GLU B 303 SHEET 1 J 2 HIS B 388 PRO B 389 0 SHEET 2 J 2 ALA B 396 PHE B 397 -1 O PHE B 397 N HIS B 388 SSBOND 1 CYS A 351 CYS A 394 1555 1555 2.07 SSBOND 2 CYS B 351 CYS B 394 1555 1555 2.05 LINK C GLU A 206 N MSE A 207 1555 1555 1.33 LINK C MSE A 207 N CYS A 208 1555 1555 1.34 LINK C TRP A 315 N MSE A 316 1555 1555 1.33 LINK C MSE A 316 N ARG A 317 1555 1555 1.34 LINK C LEU A 377 N MSE A 378 1555 1555 1.33 LINK C GLU B 206 N MSE B 207 1555 1555 1.33 LINK C MSE B 207 N CYS B 208 1555 1555 1.33 LINK C TRP B 315 N MSE B 316 1555 1555 1.33 LINK C MSE B 316 N ARG B 317 1555 1555 1.33 LINK C LEU B 377 N MSE B 378 1555 1555 1.34 LINK NE2 HIS A 406 ZN ZN A 502 1555 1555 2.12 LINK NE2 HIS A 411 ZN ZN A 502 1555 1555 2.12 LINK NE2 HIS B 406 ZN ZN B 502 1555 1555 2.12 LINK ND1 HIS B 219 ZN ZN B 501 1555 1555 2.16 LINK ND1 HIS A 219 ZN ZN A 501 1555 1555 2.16 LINK NE2 HIS B 411 ZN ZN B 502 1555 1555 2.17 LINK SG CYS A 205 ZN ZN A 501 1555 1555 2.26 LINK SG CYS A 393 ZN ZN A 502 1555 1555 2.28 LINK SG CYS A 390 ZN ZN A 502 1555 1555 2.29 LINK SG CYS B 205 ZN ZN B 501 1555 1555 2.30 LINK SG CYS A 216 ZN ZN A 501 1555 1555 2.30 LINK SG CYS B 390 ZN ZN B 502 1555 1555 2.33 LINK SG CYS B 393 ZN ZN B 502 1555 1555 2.33 LINK SG CYS A 208 ZN ZN A 501 1555 1555 2.35 LINK SG CYS B 216 ZN ZN B 501 1555 1555 2.36 LINK SG CYS B 208 ZN ZN B 501 1555 1555 2.36 CISPEP 1 GLY A 274 PRO A 275 0 7.41 CISPEP 2 GLY B 274 PRO B 275 0 5.39 SITE 1 AC1 4 CYS A 205 CYS A 208 CYS A 216 HIS A 219 SITE 1 AC2 4 CYS A 390 CYS A 393 HIS A 406 HIS A 411 SITE 1 AC3 4 CYS B 205 CYS B 208 CYS B 216 HIS B 219 SITE 1 AC4 4 CYS B 390 CYS B 393 HIS B 406 HIS B 411 CRYST1 54.734 48.782 78.713 90.00 100.05 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 0.018270 0.000000 0.003238 0.00000 SCALE2 0.000000 0.020499 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012902 0.00000