HEADER RNA BINDING PROTEIN 05-APR-23 8SCA TITLE REC3 DOMAIN FROM S. PYOGENES CAS9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: SPCAS9,SPYCAS9; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PYOGENES; SOURCE 3 ORGANISM_TAXID: 1314; SOURCE 4 GENE: CAS9, CSN1, SPY_1046; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CRISPR CAS9, NUCLEIC ACID BINDING PROTEIN, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.M.D'ORDINE,E.SKEENS,G.P.LISI,G.JOGL REVDAT 1 13-MAR-24 8SCA 0 JRNL AUTH E.SKEENS,S.SINHA,M.AHSAN,A.M.D'ORDINE,G.JOGL,G.PALERMO, JRNL AUTH 2 G.P.LISI JRNL TITL HIGH-FIDELITY, HYPER-ACCURATE, AND EVOLVED MUTANTS REWIRE JRNL TITL 2 ATOMIC-LEVEL COMMUNICATION IN CRISPR-CAS9. JRNL REF SCI ADV V. 10 L1045 2024 JRNL REFN ESSN 2375-2548 JRNL PMID 38446895 JRNL DOI 10.1126/SCIADV.ADL1045 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.V.AFONINE,R.W.GROSSE-KUNSTLEVE,N.ECHOLS,J.J.HEADD, REMARK 1 AUTH 2 N.W.MORIARTY,M.MUSTYAKIMOV,T.C.TERWILLIGER,A.URZHUMTSEV, REMARK 1 AUTH 3 P.H.ZWART,P.D.ADAMS REMARK 1 TITL TOWARDS AUTOMATED CRYSTALLOGRAPHIC STRUCTURE REFINEMENT WITH REMARK 1 TITL 2 PHENIX.REFINE. REMARK 1 REF ACTA CRYSTALLOGR., SECT. D: V. 68 352 2012 REMARK 1 REF 2 BIOL. CRYSTALLOGR. REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 1.67 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 25609 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1317 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 38.1700 - 3.4700 1.00 2876 149 0.2004 0.2053 REMARK 3 2 3.4700 - 2.7600 1.00 2729 162 0.1843 0.2103 REMARK 3 3 2.7600 - 2.4100 1.00 2715 151 0.1702 0.1685 REMARK 3 4 2.4100 - 2.1900 1.00 2676 150 0.1644 0.1827 REMARK 3 5 2.1900 - 2.0300 1.00 2689 145 0.1611 0.2221 REMARK 3 6 2.0300 - 1.9100 1.00 2674 139 0.1732 0.2188 REMARK 3 7 1.9100 - 1.8200 1.00 2682 125 0.1964 0.2026 REMARK 3 8 1.8200 - 1.7400 1.00 2649 146 0.2048 0.3087 REMARK 3 9 1.7400 - 1.6700 0.98 2602 150 0.2502 0.3005 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.182 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.032 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.72 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 : 0.006 1862 REMARK 3 ANGLE : 0.818 2484 REMARK 3 CHIRALITY : 0.052 272 REMARK 3 PLANARITY : 0.008 315 REMARK 3 DIHEDRAL : 5.754 242 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): -7.5479 8.7403 -0.3011 REMARK 3 T TENSOR REMARK 3 T11: 0.0947 T22: 0.0919 REMARK 3 T33: 0.0919 T12: 0.0119 REMARK 3 T13: -0.0031 T23: -0.0055 REMARK 3 L TENSOR REMARK 3 L11: 0.4340 L22: 0.3407 REMARK 3 L33: 0.3694 L12: -0.1241 REMARK 3 L13: -0.0368 L23: 0.1144 REMARK 3 S TENSOR REMARK 3 S11: -0.0250 S12: 0.0121 S13: 0.0099 REMARK 3 S21: 0.0793 S22: 0.0332 S23: -0.0289 REMARK 3 S31: 0.0602 S32: 0.0360 S33: -0.0047 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 8SCA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-APR-23. REMARK 100 THE DEPOSITION ID IS D_1000273428. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25725 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 43.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 13.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5, 0.2 M SODIUM REMARK 280 CHLORIDE, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K 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 26.68000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.90000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.31550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.90000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.68000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.31550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 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 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 B 1092 O HOH B 1093 1.81 REMARK 500 O HOH B 1034 O HOH B 1069 1.84 REMARK 500 OD1 ASN B 497 O HOH B 901 1.87 REMARK 500 O HOH B 995 O HOH B 1066 1.89 REMARK 500 O HOH B 939 O HOH B 1074 1.92 REMARK 500 O HOH B 908 O HOH B 909 1.98 REMARK 500 O HOH B 928 O HOH B 1068 2.02 REMARK 500 NE ARG B 654 O HOH B 902 2.03 REMARK 500 O HOH B 1017 O HOH B 1088 2.07 REMARK 500 O HOH B 929 O HOH B 1054 2.08 REMARK 500 O ARG B 635 O HOH B 903 2.10 REMARK 500 O HOH B 979 O HOH B 1089 2.12 REMARK 500 O HOH B 916 O HOH B 1059 2.12 REMARK 500 O HOH B 973 O HOH B 1076 2.13 REMARK 500 O HOH B 901 O HOH B 1022 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 1018 O HOH B 1056 2455 2.18 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 B 585 -61.82 71.21 REMARK 500 LEU B 591 57.88 -91.28 REMARK 500 ASN B 668 34.25 -147.61 REMARK 500 ASP B 686 57.75 -142.76 REMARK 500 REMARK 500 REMARK: NULL DBREF 8SCA B 497 713 UNP Q99ZW2 CAS9_STRP1 497 713 SEQADV 8SCA SER B 496 UNP Q99ZW2 EXPRESSION TAG SEQRES 1 B 218 SER ASN PHE ASP LYS ASN LEU PRO ASN GLU LYS VAL LEU SEQRES 2 B 218 PRO LYS HIS SER LEU LEU TYR GLU TYR PHE THR VAL TYR SEQRES 3 B 218 ASN GLU LEU THR LYS VAL LYS TYR VAL THR GLU GLY MET SEQRES 4 B 218 ARG LYS PRO ALA PHE LEU SER GLY GLU GLN LYS LYS ALA SEQRES 5 B 218 ILE VAL ASP LEU LEU PHE LYS THR ASN ARG LYS VAL THR SEQRES 6 B 218 VAL LYS GLN LEU LYS GLU ASP TYR PHE LYS LYS ILE GLU SEQRES 7 B 218 CYS PHE ASP SER VAL GLU ILE SER GLY VAL GLU ASP ARG SEQRES 8 B 218 PHE ASN ALA SER LEU GLY THR TYR HIS ASP LEU LEU LYS SEQRES 9 B 218 ILE ILE LYS ASP LYS ASP PHE LEU ASP ASN GLU GLU ASN SEQRES 10 B 218 GLU ASP ILE LEU GLU ASP ILE VAL LEU THR LEU THR LEU SEQRES 11 B 218 PHE GLU ASP ARG GLU MET ILE GLU GLU ARG LEU LYS THR SEQRES 12 B 218 TYR ALA HIS LEU PHE ASP ASP LYS VAL MET LYS GLN LEU SEQRES 13 B 218 LYS ARG ARG ARG TYR THR GLY TRP GLY ARG LEU SER ARG SEQRES 14 B 218 LYS LEU ILE ASN GLY ILE ARG ASP LYS GLN SER GLY LYS SEQRES 15 B 218 THR ILE LEU ASP PHE LEU LYS SER ASP GLY PHE ALA ASN SEQRES 16 B 218 ARG ASN PHE MET GLN LEU ILE HIS ASP ASP SER LEU THR SEQRES 17 B 218 PHE LYS GLU ASP ILE GLN LYS ALA GLN VAL HET EDO B 801 10 HET EDO B 802 10 HET EDO B 803 10 HET EDO B 804 10 HET EDO B 805 10 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 5(C2 H6 O2) FORMUL 7 HOH *196(H2 O) HELIX 1 AA1 SER B 512 THR B 525 1 14 HELIX 2 AA2 SER B 541 LEU B 552 1 12 HELIX 3 AA3 THR B 560 TYR B 568 1 9 HELIX 4 AA4 LEU B 591 LYS B 602 1 12 HELIX 5 AA5 ASP B 603 ASN B 609 1 7 HELIX 6 AA6 ASN B 612 PHE B 626 1 15 HELIX 7 AA7 ASP B 628 LYS B 637 1 10 HELIX 8 AA8 THR B 638 ALA B 640 5 3 HELIX 9 AA9 ASP B 644 LYS B 652 1 9 HELIX 10 AB1 SER B 663 GLY B 669 1 7 HELIX 11 AB2 THR B 678 SER B 685 1 8 HELIX 12 AB3 ASN B 692 ASP B 699 1 8 HELIX 13 AB4 THR B 703 GLN B 712 1 10 SHEET 1 AA1 2 PHE B 498 ASP B 499 0 SHEET 2 AA1 2 LEU B 502 LYS B 506 -1 O GLU B 505 N ASP B 499 SHEET 1 AA2 3 ALA B 538 PHE B 539 0 SHEET 2 AA2 3 LYS B 528 VAL B 530 -1 N TYR B 529 O ALA B 538 SHEET 3 AA2 3 GLU B 579 SER B 581 -1 O SER B 581 N LYS B 528 CRYST1 53.360 54.631 73.800 90.00 90.00 90.00 P 21 21 21 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 0.018741 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018305 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013550 0.00000