HEADER TRANSCRIPTION/DNA 29-OCT-15 5EI9 TITLE HUMAN PRDM9 ALLELE-A ZNF DOMAIN WITH ASSOCIATED RECOMBINATION HOTSPOT TITLE 2 DNA SEQUENCE I COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*AP*TP*CP*CP*AP*CP*GP*TP*GP*GP*CP*TP*AP*GP*GP*GP*AP*GP*GP*CP*C)- COMPND 4 3'); COMPND 5 CHAIN: A, C; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE PRDM9; COMPND 9 CHAIN: F, E; COMPND 10 FRAGMENT: ZNF8-12 (UNP RESIDUES 717-858); COMPND 11 SYNONYM: PR DOMAIN ZINC FINGER PROTEIN 9,PR DOMAIN-CONTAINING PROTEIN COMPND 12 9; COMPND 13 EC: 2.1.1.43; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: DNA (5'- COMPND 17 D(*TP*GP*GP*CP*CP*TP*CP*CP*CP*TP*AP*GP*CP*CP*AP*CP*GP*TP*GP*GP*A)- COMPND 18 3'); COMPND 19 CHAIN: B, D; 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 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: PRDM9, PFM6; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) CODON-PLUS RIL; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 19 ORGANISM_COMMON: HUMAN; SOURCE 20 ORGANISM_TAXID: 9606 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 5EI9 1 REMARK REVDAT 3 25-DEC-19 5EI9 1 REMARK REVDAT 2 27-SEP-17 5EI9 1 REMARK REVDAT 1 17-FEB-16 5EI9 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. 1.92 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) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 104452 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.790 REMARK 3 FREE R VALUE TEST SET COUNT : 3954 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 32.9898 - 5.8229 0.98 3629 142 0.1658 0.1532 REMARK 3 2 5.8229 - 4.6258 1.00 3682 138 0.1750 0.2193 REMARK 3 3 4.6258 - 4.0423 1.00 3670 136 0.1798 0.2370 REMARK 3 4 4.0423 - 3.6732 1.00 3688 142 0.1899 0.1954 REMARK 3 5 3.6732 - 3.4102 0.99 3683 136 0.2081 0.2312 REMARK 3 6 3.4102 - 3.2093 0.98 3633 134 0.2181 0.2325 REMARK 3 7 3.2093 - 3.0487 0.99 3620 146 0.2530 0.2976 REMARK 3 8 3.0487 - 2.9161 1.00 3680 140 0.2477 0.2498 REMARK 3 9 2.9161 - 2.8039 1.00 3742 140 0.2416 0.2351 REMARK 3 10 2.8039 - 2.7072 1.00 3674 140 0.2414 0.2718 REMARK 3 11 2.7072 - 2.6226 1.00 3565 156 0.2446 0.2766 REMARK 3 12 2.6226 - 2.5477 1.00 3738 142 0.2370 0.2398 REMARK 3 13 2.5477 - 2.4806 1.00 3716 134 0.2358 0.3112 REMARK 3 14 2.4806 - 2.4201 1.00 3666 152 0.2305 0.2494 REMARK 3 15 2.4201 - 2.3651 1.00 3687 146 0.2343 0.3297 REMARK 3 16 2.3651 - 2.3148 1.00 3676 154 0.2294 0.2552 REMARK 3 17 2.3148 - 2.2685 1.00 3778 132 0.2260 0.2354 REMARK 3 18 2.2685 - 2.2257 1.00 3512 166 0.2351 0.2754 REMARK 3 19 2.2257 - 2.1860 1.00 3784 141 0.2639 0.2848 REMARK 3 20 2.1860 - 2.1489 1.00 3629 136 0.2529 0.3220 REMARK 3 21 2.1489 - 2.1142 1.00 3652 149 0.2704 0.2673 REMARK 3 22 2.1142 - 2.0817 0.99 3748 145 0.2741 0.2781 REMARK 3 23 2.0817 - 2.0511 0.99 3550 179 0.2912 0.3130 REMARK 3 24 2.0511 - 2.0222 0.98 3610 143 0.2965 0.3191 REMARK 3 25 2.0222 - 1.9949 0.98 3601 126 0.3124 0.4072 REMARK 3 26 1.9949 - 1.9690 0.97 3654 145 0.3283 0.3238 REMARK 3 27 1.9690 - 1.9444 0.94 3422 132 0.3590 0.3842 REMARK 3 28 1.9444 - 1.9210 0.51 1809 82 0.3368 0.3911 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.120 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 3781 REMARK 3 ANGLE : 1.117 5439 REMARK 3 CHIRALITY : 0.047 570 REMARK 3 PLANARITY : 0.007 417 REMARK 3 DIHEDRAL : 25.999 1553 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 5EI9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214939. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-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) : 1.000 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 : 52634 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 32.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 24.90 REMARK 200 R MERGE (I) : 0.16000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.3900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 13.80 REMARK 200 R MERGE FOR SHELL (I) : 0.94800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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 (%): 59.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.058 M BISTRIS PROPANE, 0.042 M REMARK 280 CITRIC ACID, 25% 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: 5730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E, 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 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: 6130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -49.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: F, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 F 714 REMARK 465 SER F 715 REMARK 465 GLU F 716 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 465 GLY E 714 REMARK 465 SER E 715 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 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 F 717 CG CD CE NZ REMARK 470 THR F 826 OG1 CG2 REMARK 470 GLU E 716 CG CD OE1 OE2 REMARK 470 LYS E 717 CG CD CE NZ REMARK 470 THR E 826 OG1 CG2 REMARK 470 DT B 22 O5' 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 GLY E 783 O HOH E 1101 2.01 REMARK 500 O HOH B 108 O HOH B 122 2.03 REMARK 500 O HOH A 129 O HOH E 1150 2.05 REMARK 500 O HOH B 112 O HOH B 118 2.16 REMARK 500 OP1 DC A 11 NH2 ARG E 782 2.17 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 DG A 14 O3' DG A 14 C3' -0.038 REMARK 500 DT B 27 O3' DT B 27 C3' -0.050 REMARK 500 DT B 31 O3' DT B 31 C3' -0.050 REMARK 500 DT D 31 O3' DT D 31 C3' -0.064 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 DA A 1 C3' - C2' - C1' ANGL. DEV. = -5.5 DEGREES REMARK 500 DA A 1 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DC A 6 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG A 9 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DC A 11 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DA A 13 O4' - C1' - N9 ANGL. DEV. = 3.0 DEGREES REMARK 500 DA A 17 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DC C 11 O4' - C1' - N1 ANGL. DEV. = 1.8 DEGREES REMARK 500 DA C 13 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG C 14 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA C 17 O4' - C1' - N9 ANGL. DEV. = 3.9 DEGREES REMARK 500 DC B 29 O4' - C1' - N1 ANGL. DEV. = 3.2 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 CYS F 752 -74.21 -115.04 REMARK 500 GLN F 766 -6.59 76.92 REMARK 500 LYS E 717 -170.41 -70.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH F1131 DISTANCE = 8.69 ANGSTROMS 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 F1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS F 721 SG REMARK 620 2 CYS F 724 SG 119.1 REMARK 620 3 HIS F 737 NE2 115.9 98.4 REMARK 620 4 HIS F 741 NE2 113.8 110.6 95.7 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 95.5 REMARK 620 3 HIS F 765 NE2 111.0 78.4 REMARK 620 4 HIS F 769 NE2 134.3 108.3 111.7 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 111.2 REMARK 620 3 HIS F 793 NE2 117.2 105.7 REMARK 620 4 HIS F 797 NE2 115.4 109.4 96.6 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 123.9 REMARK 620 3 HIS F 821 NE2 119.0 92.6 REMARK 620 4 HIS F 825 NE2 127.0 95.7 88.9 REMARK 620 N 1 2 3 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 113.7 REMARK 620 3 HIS E 737 NE2 99.4 106.6 REMARK 620 4 HIS E 741 NE2 110.9 113.8 111.4 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 121.1 REMARK 620 3 HIS E 765 NE2 112.0 96.0 REMARK 620 4 HIS E 769 NE2 116.9 104.1 103.6 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 112.3 REMARK 620 3 HIS E 793 NE2 109.2 106.6 REMARK 620 4 HIS E 797 NE2 115.8 111.9 99.8 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 124.7 REMARK 620 3 HIS E 821 NE2 111.1 95.2 REMARK 620 4 HIS E 825 NE2 106.4 117.3 98.0 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 F 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN F 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN F 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN F 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN E 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN E 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN E 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN E 1004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5EGB RELATED DB: PDB REMARK 900 RELATED ID: 5EH2 RELATED DB: PDB DBREF 5EI9 A 1 21 PDB 5EI9 5EI9 1 21 DBREF 5EI9 F 716 857 UNP Q9NQV7 PRDM9_HUMAN 717 858 DBREF 5EI9 E 716 857 UNP Q9NQV7 PRDM9_HUMAN 717 858 DBREF 5EI9 C 1 21 PDB 5EI9 5EI9 1 21 DBREF 5EI9 B 22 42 PDB 5EI9 5EI9 22 42 DBREF 5EI9 D 22 42 PDB 5EI9 5EI9 22 42 SEQADV 5EI9 GLY F 714 UNP Q9NQV7 EXPRESSION TAG SEQADV 5EI9 SER F 715 UNP Q9NQV7 EXPRESSION TAG SEQADV 5EI9 GLY E 714 UNP Q9NQV7 EXPRESSION TAG SEQADV 5EI9 SER E 715 UNP Q9NQV7 EXPRESSION TAG SEQRES 1 A 21 DA DT DC DC DA DC DG DT DG DG DC DT DA SEQRES 2 A 21 DG DG DG DA DG DG DC DC 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 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 C 21 DA DT DC DC DA DC DG DT DG DG DC DT DA SEQRES 2 C 21 DG DG DG DA DG DG DC DC SEQRES 1 B 21 DT DG DG DC DC DT DC DC DC DT DA DG DC SEQRES 2 B 21 DC DA DC DG DT DG DG DA SEQRES 1 D 21 DT DG DG DC DC DT DC DC DC DT DA DG DC SEQRES 2 D 21 DC DA DC DG DT DG DG DA HET ZN F1001 1 HET ZN F1002 1 HET ZN F1003 1 HET ZN F1004 1 HET ZN E1001 1 HET ZN E1002 1 HET ZN E1003 1 HET ZN E1004 1 HETNAM ZN ZINC ION FORMUL 7 ZN 8(ZN 2+) FORMUL 15 HOH *168(H2 O) HELIX 1 AA1 ASN F 730 GLY F 743 1 14 HELIX 2 AA2 ASP F 758 HIS F 765 1 8 HELIX 3 AA3 GLN F 766 GLY F 771 1 6 HELIX 4 AA4 ASP F 786 GLY F 799 1 14 HELIX 5 AA5 ASN F 814 ARG F 823 1 10 HELIX 6 AA6 ASN E 730 ARG E 739 1 10 HELIX 7 AA7 THR E 740 THR E 742 5 3 HELIX 8 AA8 ASP E 758 GLY E 771 1 14 HELIX 9 AA9 ASP E 786 GLY E 799 1 14 HELIX 10 AB1 ASN E 814 ARG E 823 1 10 SHEET 1 AA1 2 TYR F 719 VAL F 720 0 SHEET 2 AA1 2 GLY F 727 PHE F 728 -1 O PHE F 728 N TYR F 719 SHEET 1 AA2 2 TYR F 747 VAL F 748 0 SHEET 2 AA2 2 GLY F 755 PHE F 756 -1 O PHE F 756 N TYR F 747 SHEET 1 AA3 2 TYR F 775 VAL F 776 0 SHEET 2 AA3 2 GLY F 783 PHE F 784 -1 O PHE F 784 N TYR F 775 SHEET 1 AA4 2 TYR F 803 VAL F 804 0 SHEET 2 AA4 2 GLY F 811 PHE F 812 -1 O PHE F 812 N TYR F 803 SHEET 1 AA5 2 TYR E 719 VAL E 720 0 SHEET 2 AA5 2 GLY E 727 PHE E 728 -1 O PHE E 728 N TYR E 719 SHEET 1 AA6 2 TYR E 747 VAL E 748 0 SHEET 2 AA6 2 GLY E 755 PHE E 756 -1 O PHE E 756 N TYR E 747 SHEET 1 AA7 2 TYR E 775 VAL E 776 0 SHEET 2 AA7 2 GLY E 783 PHE E 784 -1 O PHE E 784 N TYR E 775 SHEET 1 AA8 2 TYR E 803 VAL E 804 0 SHEET 2 AA8 2 GLY E 811 PHE E 812 -1 O PHE E 812 N TYR E 803 LINK SG CYS F 721 ZN ZN F1001 1555 1555 2.18 LINK SG CYS F 724 ZN ZN F1001 1555 1555 2.22 LINK NE2 HIS F 737 ZN ZN F1001 1555 1555 2.08 LINK NE2 HIS F 741 ZN ZN F1001 1555 1555 1.83 LINK SG CYS F 749 ZN ZN F1002 1555 1555 2.43 LINK SG CYS F 752 ZN ZN F1002 1555 1555 2.02 LINK NE2 HIS F 765 ZN ZN F1002 1555 1555 2.38 LINK NE2 HIS F 769 ZN ZN F1002 1555 1555 2.01 LINK SG CYS F 777 ZN ZN F1003 1555 1555 2.00 LINK SG CYS F 780 ZN ZN F1003 1555 1555 2.28 LINK NE2 HIS F 793 ZN ZN F1003 1555 1555 1.99 LINK NE2 HIS F 797 ZN ZN F1003 1555 1555 2.01 LINK SG CYS F 805 ZN ZN F1004 1555 1555 2.25 LINK SG CYS F 808 ZN ZN F1004 1555 1555 2.20 LINK NE2 HIS F 821 ZN ZN F1004 1555 1555 2.19 LINK NE2 HIS F 825 ZN ZN F1004 1555 1555 2.32 LINK SG CYS E 721 ZN ZN E1001 1555 1555 2.31 LINK SG CYS E 724 ZN ZN E1001 1555 1555 2.21 LINK NE2 HIS E 737 ZN ZN E1001 1555 1555 1.92 LINK NE2 HIS E 741 ZN ZN E1001 1555 1555 2.13 LINK SG CYS E 749 ZN ZN E1002 1555 1555 2.19 LINK SG CYS E 752 ZN ZN E1002 1555 1555 2.04 LINK NE2 HIS E 765 ZN ZN E1002 1555 1555 2.11 LINK NE2 HIS E 769 ZN ZN E1002 1555 1555 2.11 LINK SG CYS E 777 ZN ZN E1003 1555 1555 2.12 LINK SG CYS E 780 ZN ZN E1003 1555 1555 2.32 LINK NE2 HIS E 793 ZN ZN E1003 1555 1555 1.92 LINK NE2 HIS E 797 ZN ZN E1003 1555 1555 2.04 LINK SG CYS E 805 ZN ZN E1004 1555 1555 2.28 LINK SG CYS E 808 ZN ZN E1004 1555 1555 2.19 LINK NE2 HIS E 821 ZN ZN E1004 1555 1555 2.12 LINK NE2 HIS E 825 ZN ZN E1004 1555 1555 2.20 SITE 1 AC1 4 CYS F 721 CYS F 724 HIS F 737 HIS F 741 SITE 1 AC2 4 CYS F 749 CYS F 752 HIS F 765 HIS F 769 SITE 1 AC3 4 CYS F 777 CYS F 780 HIS F 793 HIS F 797 SITE 1 AC4 4 CYS F 805 CYS F 808 HIS F 821 HIS F 825 SITE 1 AC5 4 CYS E 721 CYS E 724 HIS E 737 HIS E 741 SITE 1 AC6 4 CYS E 749 CYS E 752 HIS E 765 HIS E 769 SITE 1 AC7 4 CYS E 777 CYS E 780 HIS E 793 HIS E 797 SITE 1 AC8 4 CYS E 805 CYS E 808 HIS E 821 HIS E 825 CRYST1 44.329 55.740 76.038 89.85 75.50 86.58 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 0.022559 -0.001347 -0.005853 0.00000 SCALE2 0.000000 0.017972 0.000229 0.00000 SCALE3 0.000000 0.000000 0.013585 0.00000