HEADER DNA BINDING PROTEIN 05-MAY-21 7MPZ TITLE HNH NUCLEASE DOMAIN FROM G. STEAROTHERMOPHILUS CAS9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRISPR-ASSOCIATED ENDONUCLEASE CAS9; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GEOBACILLUS STEAROTHERMOPHILUS; SOURCE 3 ORGANISM_COMMON: BACILLUS STEAROTHERMOPHILUS; SOURCE 4 ORGANISM_TAXID: 1422; SOURCE 5 GENE: CAS9, GS458_0313; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NUCLEASE DOMAIN, CRISPR CAS9, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.M.D'ORDINE,H.B.BELATO,G.P.LISI,G.JOGL REVDAT 2 18-OCT-23 7MPZ 1 REMARK REVDAT 1 22-DEC-21 7MPZ 0 JRNL AUTH H.B.BELATO,A.M.D'ORDINE,L.NIERZWICKI,P.R.ARANTES,G.JOGL, JRNL AUTH 2 G.PALERMO,G.P.LISI JRNL TITL STRUCTURAL AND DYNAMIC INSIGHTS INTO THE HNH NUCLEASE OF JRNL TITL 2 DIVERGENT CAS9 SPECIES. JRNL REF J.STRUCT.BIOL. V. 214 07814 2021 JRNL REFN ESSN 1095-8657 JRNL PMID 34871741 JRNL DOI 10.1016/J.JSB.2021.107814 REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17RC4_3626 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 24716 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 1201 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 38.7600 - 4.2400 1.00 2620 136 0.1658 0.2045 REMARK 3 2 4.2400 - 3.3700 1.00 2607 134 0.1741 0.2325 REMARK 3 3 3.3700 - 2.9400 1.00 2618 112 0.2072 0.2277 REMARK 3 4 2.9400 - 2.6700 1.00 2613 148 0.2097 0.2425 REMARK 3 5 2.6700 - 2.4800 1.00 2570 163 0.2115 0.2477 REMARK 3 6 2.4800 - 2.3400 1.00 2644 113 0.2301 0.3241 REMARK 3 7 2.3300 - 2.2200 1.00 2629 130 0.2381 0.2747 REMARK 3 8 2.2200 - 2.1200 1.00 2593 147 0.2419 0.3220 REMARK 3 9 2.1200 - 2.0400 0.99 2621 118 0.2610 0.2805 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) : 0.217 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.252 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.48 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 : 0.007 1184 REMARK 3 ANGLE : 0.817 1592 REMARK 3 CHIRALITY : 0.046 169 REMARK 3 PLANARITY : 0.006 206 REMARK 3 DIHEDRAL : 17.596 468 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -16.5147 -0.4019 -3.7387 REMARK 3 T TENSOR REMARK 3 T11: 0.3666 T22: 0.3233 REMARK 3 T33: 0.3598 T12: -0.0108 REMARK 3 T13: -0.0204 T23: -0.0656 REMARK 3 L TENSOR REMARK 3 L11: 1.0708 L22: 1.5641 REMARK 3 L33: 2.9686 L12: -0.3171 REMARK 3 L13: -0.4276 L23: 0.7899 REMARK 3 S TENSOR REMARK 3 S11: 0.0763 S12: 0.2357 S13: -0.0777 REMARK 3 S21: -0.1151 S22: -0.1617 S23: 0.3307 REMARK 3 S31: -0.4053 S32: -0.2278 S33: 0.0494 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 7MPZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-MAY-21. REMARK 100 THE DEPOSITION ID IS D_1000256250. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-SEP-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-003 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541780 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24738 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 38.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.3100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6J9N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.12 M [0.3 M DIETHYLENE GLYCOL, 0.3 M REMARK 280 TRIETHYLENE GLYCOL, 0.3 M TETRAETHYLENE GLYCOL, 0.3 M REMARK 280 PENTAETHYLENE GLYCOL], 0.1 M [MES AND IMIDAZOLE] PH 6.5, 30% (V/ REMARK 280 V) [40% (V/V) GLYCEROL, 20% (W/V) POLYETHYLENE GLYCOL 4000], REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.69650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.97800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.97800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.84825 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.97800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.97800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 89.54475 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.97800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.97800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.84825 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.97800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.97800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 89.54475 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.69650 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 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 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 -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 REMARK 465 GLU A 1 REMARK 465 ARG A 2 REMARK 465 ASP A 141 REMARK 465 GLU A 142 REMARK 465 ASN A 143 REMARK 465 GLU A 144 REMARK 465 GLU A 145 REMARK 465 THR A 146 REMARK 465 GLU A 147 REMARK 465 PHE A 148 REMARK 465 LYS A 149 REMARK 465 ASN A 150 REMARK 465 ARG A 151 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 A 219 O HOH A 230 2.10 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 LEU A 80 28.50 49.71 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 A 267 DISTANCE = 6.47 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6J9N RELATED DB: PDB REMARK 900 RELATED ID: 6O56 RELATED DB: PDB DBREF1 7MPZ A 1 151 UNP A0A250DVH8_GEOSE DBREF2 7MPZ A A0A250DVH8 511 661 SEQADV 7MPZ GLY A -2 UNP A0A250DVH EXPRESSION TAG SEQADV 7MPZ HIS A -1 UNP A0A250DVH EXPRESSION TAG SEQADV 7MPZ MET A 0 UNP A0A250DVH EXPRESSION TAG SEQRES 1 A 154 GLY HIS MET GLU ARG ARG LYS THR LYS LYS GLU GLN ASP SEQRES 2 A 154 GLU ASN ARG LYS LYS ASN GLU THR ALA ILE ARG GLN LEU SEQRES 3 A 154 MET GLU TYR GLY LEU THR LEU ASN PRO THR GLY HIS ASP SEQRES 4 A 154 ILE VAL LYS PHE LYS LEU TRP SER GLU GLN ASN GLY ARG SEQRES 5 A 154 CYS ALA TYR SER LEU GLN PRO ILE GLU ILE GLU ARG LEU SEQRES 6 A 154 LEU GLU PRO GLY TYR VAL GLU VAL ASP HIS VAL ILE PRO SEQRES 7 A 154 TYR SER ARG SER LEU ASP ASP SER TYR THR ASN LYS VAL SEQRES 8 A 154 LEU VAL LEU THR ARG GLU ASN ARG GLU LYS GLY ASN ARG SEQRES 9 A 154 ILE PRO ALA GLU TYR LEU GLY VAL GLY THR GLU ARG TRP SEQRES 10 A 154 GLN GLN PHE GLU THR PHE VAL LEU THR ASN LYS GLN PHE SEQRES 11 A 154 SER LYS LYS LYS ARG ASP ARG LEU LEU ARG LEU HIS TYR SEQRES 12 A 154 ASP GLU ASN GLU GLU THR GLU PHE LYS ASN ARG FORMUL 2 HOH *67(H2 O) HELIX 1 AA1 ARG A 3 TYR A 26 1 24 HELIX 2 AA2 THR A 33 GLN A 46 1 14 HELIX 3 AA3 GLU A 58 LEU A 62 5 5 HELIX 4 AA4 PRO A 75 LEU A 80 1 6 HELIX 5 AA5 SER A 83 THR A 85 5 3 HELIX 6 AA6 THR A 92 GLY A 99 1 8 HELIX 7 AA7 ILE A 102 GLY A 108 1 7 HELIX 8 AA8 THR A 111 THR A 123 1 13 HELIX 9 AA9 SER A 128 ARG A 137 1 10 SHEET 1 AA1 2 VAL A 68 HIS A 72 0 SHEET 2 AA1 2 LYS A 87 LEU A 91 -1 O VAL A 88 N ASP A 71 CRYST1 57.956 57.956 119.393 90.00 90.00 90.00 P 41 21 2 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 0.017254 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017254 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008376 0.00000