PDB Short entry for 5EH2 HEADER TRANSCRIPTION/DNA 27-OCT-15 5EH2 TITLE HUMAN PRDM9 ALLELE-A ZNF DOMAIN WITH ASSOCIATED RECOMBINATION HOTSPOT TITLE 2 DNA SEQUENCE III COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*AP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*CP*TP*C)- COMPND 4 3'); COMPND 5 CHAIN: C, A; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(*TP*GP*AP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*G)- COMPND 10 3'); COMPND 11 CHAIN: D, B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE PRDM9; COMPND 15 CHAIN: E, F; COMPND 16 FRAGMENT: ZNF8-12 (UNP RESIDUES 717-858); COMPND 17 SYNONYM: PR DOMAIN ZINC FINGER PROTEIN 9,PR DOMAIN-CONTAINING PROTEIN COMPND 18 9; COMPND 19 EC: 2.1.1.43; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 VARIANT: ALELLE-A; SOURCE 16 GENE: PRDM9, PFM6; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 19 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) CODON-PLUS RIL; SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 21 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1 KEYWDS PROTEIN-DNA COMPLEX, RECOMBINATION, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.PATEL,J.R.HORTON,G.G.WILSON,X.ZHANG,X.CHENG REVDAT 4 06-MAR-24 5EH2 1 REMARK REVDAT 3 25-DEC-19 5EH2 1 REMARK REVDAT 2 27-SEP-17 5EH2 1 REMARK REVDAT 1 17-FEB-16 5EH2 0 JRNL AUTH A.PATEL,J.R.HORTON,G.G.WILSON,X.ZHANG,X.CHENG JRNL TITL STRUCTURAL BASIS FOR HUMAN PRDM9 ACTION AT RECOMBINATION HOT JRNL TITL 2 SPOTS. JRNL REF GENES DEV. V. 30 257 2016 JRNL REFN ISSN 0890-9369 JRNL PMID 26833727 JRNL DOI 10.1101/GAD.274928.115 REMARK 2 REMARK 2 RESOLUTION. 2.05 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.7 REMARK 3 NUMBER OF REFLECTIONS : 41843 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 1983 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 32.7510 - 4.9262 0.77 2435 126 0.1580 0.1957 REMARK 3 2 4.9262 - 3.9121 0.93 2972 151 0.1666 0.1780 REMARK 3 3 3.9121 - 3.4182 0.94 2998 142 0.1889 0.2162 REMARK 3 4 3.4182 - 3.1059 0.95 3057 143 0.2150 0.2577 REMARK 3 5 3.1059 - 2.8835 0.97 3050 156 0.2451 0.2919 REMARK 3 6 2.8835 - 2.7136 0.97 3105 150 0.2357 0.2448 REMARK 3 7 2.7136 - 2.5777 0.97 3070 156 0.2313 0.2721 REMARK 3 8 2.5777 - 2.4655 0.96 3030 156 0.2257 0.2708 REMARK 3 9 2.4655 - 2.3707 0.94 2993 155 0.2232 0.2696 REMARK 3 10 2.3707 - 2.2889 0.92 2929 140 0.2339 0.3211 REMARK 3 11 2.2889 - 2.2173 0.88 2810 137 0.2929 0.3461 REMARK 3 12 2.2173 - 2.1540 0.85 2691 140 0.2833 0.3076 REMARK 3 13 2.1540 - 2.0973 0.81 2607 132 0.2957 0.2758 REMARK 3 14 2.0973 - 2.0461 0.67 2113 99 0.3213 0.3719 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.610 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 3777 REMARK 3 ANGLE : 1.161 5434 REMARK 3 CHIRALITY : 0.054 570 REMARK 3 PLANARITY : 0.007 416 REMARK 3 DIHEDRAL : 24.642 1555 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5EH2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214886. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41966 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 32.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.4 REMARK 200 DATA REDUNDANCY : 1.800 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.8 REMARK 200 DATA REDUNDANCY IN SHELL : 1.60 REMARK 200 R MERGE FOR SHELL (I) : 0.45600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: ZN SAD DETERMINED STRUCTURE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.058 M BISTRIS PROPANE, 0.042 M REMARK 280 CITRIC ACID, 20% PEG3350, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, F 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E 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 E 714 REMARK 465 SER E 715 REMARK 465 GLU E 716 REMARK 465 GLY E 827 REMARK 465 GLU E 828 REMARK 465 LYS E 829 REMARK 465 PRO E 830 REMARK 465 TYR E 831 REMARK 465 VAL E 832 REMARK 465 CYS E 833 REMARK 465 ARG E 834 REMARK 465 GLU E 835 REMARK 465 CYS E 836 REMARK 465 GLY E 837 REMARK 465 ARG E 838 REMARK 465 GLY E 839 REMARK 465 PHE E 840 REMARK 465 ARG E 841 REMARK 465 ASN E 842 REMARK 465 LYS E 843 REMARK 465 SER E 844 REMARK 465 HIS E 845 REMARK 465 LEU E 846 REMARK 465 LEU E 847 REMARK 465 ARG E 848 REMARK 465 HIS E 849 REMARK 465 GLN E 850 REMARK 465 ARG E 851 REMARK 465 THR E 852 REMARK 465 HIS E 853 REMARK 465 THR E 854 REMARK 465 GLY E 855 REMARK 465 GLU E 856 REMARK 465 LYS E 857 REMARK 465 GLY F 714 REMARK 465 SER F 715 REMARK 465 GLU F 716 REMARK 465 LYS F 717 REMARK 465 GLY F 827 REMARK 465 GLU F 828 REMARK 465 LYS F 829 REMARK 465 PRO F 830 REMARK 465 TYR F 831 REMARK 465 VAL F 832 REMARK 465 CYS F 833 REMARK 465 ARG F 834 REMARK 465 GLU F 835 REMARK 465 CYS F 836 REMARK 465 GLY F 837 REMARK 465 ARG F 838 REMARK 465 GLY F 839 REMARK 465 PHE F 840 REMARK 465 ARG F 841 REMARK 465 ASN F 842 REMARK 465 LYS F 843 REMARK 465 SER F 844 REMARK 465 HIS F 845 REMARK 465 LEU F 846 REMARK 465 LEU F 847 REMARK 465 ARG F 848 REMARK 465 HIS F 849 REMARK 465 GLN F 850 REMARK 465 ARG F 851 REMARK 465 THR F 852 REMARK 465 HIS F 853 REMARK 465 THR F 854 REMARK 465 GLY F 855 REMARK 465 GLU F 856 REMARK 465 LYS F 857 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 E 717 CG CD CE NZ REMARK 470 THR E 826 OG1 CG2 REMARK 470 TYR F 719 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS F 731 CG CD CE NZ REMARK 470 THR F 826 OG1 CG2 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 HOH C 121 O HOH D 112 2.03 REMARK 500 O HOH C 112 O HOH F 1139 2.08 REMARK 500 O HOH D 108 O HOH F 1116 2.16 REMARK 500 OP1 DG C 13 O HOH C 101 2.17 REMARK 500 O2 DC C 2 N2 DG D 21 2.17 REMARK 500 OP2 DG C 7 O HOH C 102 2.18 REMARK 500 O HOH C 118 O HOH C 120 2.19 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 DA C 11 O3' DA C 11 C3' -0.057 REMARK 500 DG C 12 O5' DG C 12 C5' -0.163 REMARK 500 DG C 12 O3' DG C 12 C3' -0.084 REMARK 500 DA A 11 O3' DA A 11 C3' -0.043 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DG C 5 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG C 8 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC C 9 O5' - P - OP2 ANGL. DEV. = -12.7 DEGREES REMARK 500 DC C 9 O4' - C4' - C3' ANGL. DEV. = -3.9 DEGREES REMARK 500 DC C 9 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA C 11 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG C 12 O5' - P - OP1 ANGL. DEV. = -6.2 DEGREES REMARK 500 DA C 15 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC D 10 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG A 8 O4' - C1' - N9 ANGL. DEV. = 2.6 DEGREES REMARK 500 DC A 9 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA A 11 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DG A 12 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA A 15 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC B 11 O4' - C1' - N1 ANGL. DEV. = 2.4 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 HIS E 825 -71.84 -86.26 REMARK 500 ASN F 730 144.96 71.48 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 E1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 721 SG REMARK 620 2 CYS E 724 SG 120.9 REMARK 620 3 HIS E 737 NE2 106.5 104.6 REMARK 620 4 HIS E 741 NE2 102.7 119.6 100.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN E1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 749 SG REMARK 620 2 CYS E 752 SG 114.4 REMARK 620 3 HIS E 765 NE2 99.5 95.8 REMARK 620 4 HIS E 769 NE2 110.8 119.4 114.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN E1003 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 777 SG REMARK 620 2 CYS E 780 SG 115.5 REMARK 620 3 HIS E 793 NE2 123.8 98.1 REMARK 620 4 HIS E 797 NE2 116.2 109.3 90.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN E1004 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS E 805 SG REMARK 620 2 CYS E 808 SG 144.3 REMARK 620 3 HIS E 821 NE2 118.8 88.5 REMARK 620 4 HIS E 825 NE2 107.9 91.4 93.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN F1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS F 721 SG REMARK 620 2 CYS F 724 SG 111.2 REMARK 620 3 HIS F 737 NE2 97.5 101.9 REMARK 620 4 HIS F 741 NE2 114.0 119.0 110.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN F1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS F 749 SG REMARK 620 2 CYS F 752 SG 126.1 REMARK 620 3 HIS F 765 NE2 108.4 94.9 REMARK 620 4 HIS F 769 NE2 112.6 110.3 99.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN F1003 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS F 777 SG REMARK 620 2 CYS F 780 SG 115.8 REMARK 620 3 HIS F 793 NE2 114.1 103.1 REMARK 620 4 HIS F 797 NE2 111.1 111.9 99.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN F1004 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS F 805 SG REMARK 620 2 CYS F 808 SG 120.8 REMARK 620 3 HIS F 821 NE2 108.8 102.8 REMARK 620 4 HIS F 825 NE2 104.0 120.9 96.2 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 E 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN E 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN E 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN E 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN F 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN F 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN F 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN F 1004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5EGB RELATED DB: PDB REMARK 900 RELATED ID: 5EI9 RELATED DB: PDB DBREF 5EH2 C 1 21 PDB 5EH2 5EH2 1 21 DBREF 5EH2 D 1 21 PDB 5EH2 5EH2 1 21 DBREF 5EH2 A 1 21 PDB 5EH2 5EH2 1 21 DBREF 5EH2 B 1 21 PDB 5EH2 5EH2 1 21 DBREF 5EH2 E 716 857 UNP Q9NQV7 PRDM9_HUMAN 717 858 DBREF 5EH2 F 716 857 UNP Q9NQV7 PRDM9_HUMAN 717 858 SEQADV 5EH2 GLY E 714 UNP Q9NQV7 EXPRESSION TAG SEQADV 5EH2 SER E 715 UNP Q9NQV7 EXPRESSION TAG SEQADV 5EH2 GLY F 714 UNP Q9NQV7 EXPRESSION TAG SEQADV 5EH2 SER F 715 UNP Q9NQV7 EXPRESSION TAG SEQRES 1 C 21 DA DC DA DC DG DT DG DG DC DT DA DG DG SEQRES 2 C 21 DG DA DG DG DC DC DT DC SEQRES 1 D 21 DT DG DA DG DG DC DC DT DC DC DC DT DA SEQRES 2 D 21 DG DC DC DA DC DG DT DG SEQRES 1 A 21 DA DC DA DC DG DT DG DG DC DT DA DG DG SEQRES 2 A 21 DG DA DG DG DC DC DT DC SEQRES 1 B 21 DT DG DA DG DG DC DC DT DC DC DC DT DA SEQRES 2 B 21 DG DC DC DA DC DG DT DG SEQRES 1 E 144 GLY SER GLU LYS PRO TYR VAL CYS ARG GLU CYS GLY ARG SEQRES 2 E 144 GLY PHE SER ASN LYS SER HIS LEU LEU ARG HIS GLN ARG SEQRES 3 E 144 THR HIS THR GLY GLU LYS PRO TYR VAL CYS ARG GLU CYS SEQRES 4 E 144 GLY ARG GLY PHE ARG ASP LYS SER HIS LEU LEU ARG HIS SEQRES 5 E 144 GLN ARG THR HIS THR GLY GLU LYS PRO TYR VAL CYS ARG SEQRES 6 E 144 GLU CYS GLY ARG GLY PHE ARG ASP LYS SER ASN LEU LEU SEQRES 7 E 144 SER HIS GLN ARG THR HIS THR GLY GLU LYS PRO TYR VAL SEQRES 8 E 144 CYS ARG GLU CYS GLY ARG GLY PHE SER ASN LYS SER HIS SEQRES 9 E 144 LEU LEU ARG HIS GLN ARG THR HIS THR GLY GLU LYS PRO SEQRES 10 E 144 TYR VAL CYS ARG GLU CYS GLY ARG GLY PHE ARG ASN LYS SEQRES 11 E 144 SER HIS LEU LEU ARG HIS GLN ARG THR HIS THR GLY GLU SEQRES 12 E 144 LYS SEQRES 1 F 144 GLY SER GLU LYS PRO TYR VAL CYS ARG GLU CYS GLY ARG SEQRES 2 F 144 GLY PHE SER ASN LYS SER HIS LEU LEU ARG HIS GLN ARG SEQRES 3 F 144 THR HIS THR GLY GLU LYS PRO TYR VAL CYS ARG GLU CYS SEQRES 4 F 144 GLY ARG GLY PHE ARG ASP LYS SER HIS LEU LEU ARG HIS SEQRES 5 F 144 GLN ARG THR HIS THR GLY GLU LYS PRO TYR VAL CYS ARG SEQRES 6 F 144 GLU CYS GLY ARG GLY PHE ARG ASP LYS SER ASN LEU LEU SEQRES 7 F 144 SER HIS GLN ARG THR HIS THR GLY GLU LYS PRO TYR VAL SEQRES 8 F 144 CYS ARG GLU CYS GLY ARG GLY PHE SER ASN LYS SER HIS SEQRES 9 F 144 LEU LEU ARG HIS GLN ARG THR HIS THR GLY GLU LYS PRO SEQRES 10 F 144 TYR VAL CYS ARG GLU CYS GLY ARG GLY PHE ARG ASN LYS SEQRES 11 F 144 SER HIS LEU LEU ARG HIS GLN ARG THR HIS THR GLY GLU SEQRES 12 F 144 LYS HET ZN E1001 1 HET ZN E1002 1 HET ZN E1003 1 HET ZN E1004 1 HET ZN F1001 1 HET ZN F1002 1 HET ZN F1003 1 HET ZN F1004 1 HETNAM ZN ZINC ION FORMUL 7 ZN 8(ZN 2+) FORMUL 15 HOH *122(H2 O) HELIX 1 AA1 ASN E 730 GLY E 743 1 14 HELIX 2 AA2 ASP E 758 GLY E 771 1 14 HELIX 3 AA3 ASP E 786 GLY E 799 1 14 HELIX 4 AA4 ASN E 814 ARG E 823 1 10 HELIX 5 AA5 ASN F 730 ARG F 739 1 10 HELIX 6 AA6 THR F 740 THR F 742 5 3 HELIX 7 AA7 ASP F 758 GLY F 771 1 14 HELIX 8 AA8 ASP F 786 GLY F 799 1 14 HELIX 9 AA9 ASN F 814 ARG F 823 1 10 SHEET 1 AA1 2 TYR E 719 VAL E 720 0 SHEET 2 AA1 2 GLY E 727 PHE E 728 -1 O PHE E 728 N TYR E 719 SHEET 1 AA2 2 TYR E 747 VAL E 748 0 SHEET 2 AA2 2 GLY E 755 PHE E 756 -1 O PHE E 756 N TYR E 747 SHEET 1 AA3 2 TYR E 775 VAL E 776 0 SHEET 2 AA3 2 GLY E 783 PHE E 784 -1 O PHE E 784 N TYR E 775 SHEET 1 AA4 2 TYR E 803 VAL E 804 0 SHEET 2 AA4 2 GLY E 811 PHE E 812 -1 O PHE E 812 N TYR E 803 SHEET 1 AA5 2 TYR F 719 VAL F 720 0 SHEET 2 AA5 2 GLY F 727 PHE F 728 -1 O PHE F 728 N TYR F 719 SHEET 1 AA6 2 TYR F 747 VAL F 748 0 SHEET 2 AA6 2 GLY F 755 PHE F 756 -1 O PHE F 756 N TYR F 747 SHEET 1 AA7 2 TYR F 775 VAL F 776 0 SHEET 2 AA7 2 GLY F 783 PHE F 784 -1 O PHE F 784 N TYR F 775 SHEET 1 AA8 2 TYR F 803 VAL F 804 0 SHEET 2 AA8 2 GLY F 811 PHE F 812 -1 O PHE F 812 N TYR F 803 LINK SG CYS E 721 ZN ZN E1001 1555 1555 2.23 LINK SG CYS E 724 ZN ZN E1001 1555 1555 2.15 LINK NE2 HIS E 737 ZN ZN E1001 1555 1555 2.08 LINK NE2 HIS E 741 ZN ZN E1001 1555 1555 1.89 LINK SG CYS E 749 ZN ZN E1002 1555 1555 2.24 LINK SG CYS E 752 ZN ZN E1002 1555 1555 2.05 LINK NE2 HIS E 765 ZN ZN E1002 1555 1555 2.26 LINK NE2 HIS E 769 ZN ZN E1002 1555 1555 2.04 LINK SG CYS E 777 ZN ZN E1003 1555 1555 2.15 LINK SG CYS E 780 ZN ZN E1003 1555 1555 2.24 LINK NE2 HIS E 793 ZN ZN E1003 1555 1555 2.12 LINK NE2 HIS E 797 ZN ZN E1003 1555 1555 1.99 LINK SG CYS E 805 ZN ZN E1004 1555 1555 2.23 LINK SG CYS E 808 ZN ZN E1004 1555 1555 2.44 LINK NE2 HIS E 821 ZN ZN E1004 1555 1555 2.37 LINK NE2 HIS E 825 ZN ZN E1004 1555 1555 2.29 LINK SG CYS F 721 ZN ZN F1001 1555 1555 2.36 LINK SG CYS F 724 ZN ZN F1001 1555 1555 2.22 LINK NE2 HIS F 737 ZN ZN F1001 1555 1555 1.90 LINK NE2 HIS F 741 ZN ZN F1001 1555 1555 2.12 LINK SG CYS F 749 ZN ZN F1002 1555 1555 2.24 LINK SG CYS F 752 ZN ZN F1002 1555 1555 2.14 LINK NE2 HIS F 765 ZN ZN F1002 1555 1555 2.21 LINK NE2 HIS F 769 ZN ZN F1002 1555 1555 2.19 LINK SG CYS F 777 ZN ZN F1003 1555 1555 2.14 LINK SG CYS F 780 ZN ZN F1003 1555 1555 2.32 LINK NE2 HIS F 793 ZN ZN F1003 1555 1555 1.98 LINK NE2 HIS F 797 ZN ZN F1003 1555 1555 2.07 LINK SG CYS F 805 ZN ZN F1004 1555 1555 2.22 LINK SG CYS F 808 ZN ZN F1004 1555 1555 2.22 LINK NE2 HIS F 821 ZN ZN F1004 1555 1555 2.10 LINK NE2 HIS F 825 ZN ZN F1004 1555 1555 2.03 SITE 1 AC1 4 CYS E 721 CYS E 724 HIS E 737 HIS E 741 SITE 1 AC2 4 CYS E 749 CYS E 752 HIS E 765 HIS E 769 SITE 1 AC3 4 CYS E 777 CYS E 780 HIS E 793 HIS E 797 SITE 1 AC4 4 CYS E 805 CYS E 808 HIS E 821 HIS E 825 SITE 1 AC5 4 CYS F 721 CYS F 724 HIS F 737 HIS F 741 SITE 1 AC6 4 CYS F 749 CYS F 752 HIS F 765 HIS F 769 SITE 1 AC7 4 CYS F 777 CYS F 780 HIS F 793 HIS F 797 SITE 1 AC8 4 CYS F 805 CYS F 808 HIS F 821 HIS F 825 CRYST1 45.208 57.756 76.206 90.15 75.30 83.30 P 1 2 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 0.022120 -0.002598 -0.005895 0.00000 SCALE2 0.000000 0.017433 0.000586 0.00000 SCALE3 0.000000 0.000000 0.013574 0.00000