HEADER STRUCTURAL PROTEIN 16-FEB-23 8IF0 TITLE NMEHNH-ACRIIC1 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRISPR-ASSOCIATED ENDONUCLEASE CAS9; COMPND 3 CHAIN: X; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ANTI-CRISPR PROTEIN (ACRIIC1); COMPND 7 CHAIN: Y; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 3 ORGANISM_TAXID: 487; SOURCE 4 GENE: CAS9; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: NEISSERIA MENINGITIDIS; SOURCE 9 ORGANISM_TAXID: 487; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.L.ZHU REVDAT 1 24-APR-24 8IF0 0 JRNL AUTH Y.L.ZHU JRNL TITL INHIBITION MECHANISM OF CRISPR-CAS9 BY ANTI-CRISPR PROTEIN JRNL TITL 2 ACRIIC1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 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) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 34393 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.82 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 2010 REMARK 3 ANGLE : 0.738 2694 REMARK 3 CHIRALITY : 0.047 265 REMARK 3 PLANARITY : 0.004 353 REMARK 3 DIHEDRAL : 22.954 784 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 8IF0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 21-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1300035150. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-17 REMARK 200 TEMPERATURE (KELVIN) : 193 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9785 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34393 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.09200 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M MES, PH REMARK 280 6.2, 26% PEG3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 46.53050 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.37100 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 46.53050 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.37100 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, Y 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH X 717 LIES ON A SPECIAL POSITION. 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 GLU X 508 REMARK 465 VAL X 509 REMARK 465 LYS X 663 REMARK 465 GLU X 664 REMARK 465 ARG X 665 REMARK 465 ASN X 666 REMARK 465 LEU X 667 REMARK 465 MET Y 1 REMARK 465 ALA Y 2 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 OE1 GLU Y 49 O HOH Y 101 1.81 REMARK 500 O HOH Y 103 O HOH Y 112 1.96 REMARK 500 OH TYR Y 70 O HOH Y 102 2.02 REMARK 500 O HOH X 737 O HOH X 790 2.03 REMARK 500 O HOH X 738 O HOH X 771 2.07 REMARK 500 O HOH X 768 O HOH X 789 2.10 REMARK 500 O ASP X 598 O HOH X 701 2.10 REMARK 500 OE1 GLU X 631 O HOH X 702 2.16 REMARK 500 O HOH X 764 O HOH X 792 2.17 REMARK 500 OD1 ASP Y 50 O HOH Y 103 2.18 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 X 784 O HOH X 785 4555 1.98 REMARK 500 O HOH X 776 O HOH X 776 2656 2.14 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 TRP X 596 18.72 58.79 REMARK 500 ARG X 643 36.26 -93.89 REMARK 500 ASP Y 15 43.91 -145.83 REMARK 500 REMARK 500 REMARK: NULL DBREF 8IF0 X 508 667 UNP X5EPV9 X5EPV9_NEIME 508 667 DBREF1 8IF0 Y 1 86 UNP A0A2D0TCG3_NEIME DBREF2 8IF0 Y A0A2D0TCG3 1 86 SEQADV 8IF0 MET X 518 UNP X5EPV9 GLU 518 CONFLICT SEQADV 8IF0 MET X 522 UNP X5EPV9 ARG 522 CONFLICT SEQADV 8IF0 MET X 561 UNP X5EPV9 GLN 561 CONFLICT SEQRES 1 X 160 GLU VAL GLY LYS SER PHE LYS ASP ARG LYS MET ILE GLU SEQRES 2 X 160 LYS MET GLN GLU GLU ASN ARG LYS ASP ARG GLU LYS ALA SEQRES 3 X 160 ALA ALA LYS PHE ARG GLU TYR PHE PRO ASN PHE VAL GLY SEQRES 4 X 160 GLU PRO LYS SER LYS ASP ILE LEU LYS LEU ARG LEU TYR SEQRES 5 X 160 GLU MET GLN HIS GLY LYS CYS LEU TYR SER GLY LYS GLU SEQRES 6 X 160 ILE ASN LEU GLY ARG LEU ASN GLU LYS GLY TYR VAL GLU SEQRES 7 X 160 ILE ASP HIS ALA LEU PRO PHE SER ARG THR TRP ASP ASP SEQRES 8 X 160 SER PHE ASN ASN LYS VAL LEU VAL LEU GLY SER GLU ASN SEQRES 9 X 160 GLN ASN LYS GLY ASN GLN THR PRO TYR GLU TYR PHE ASN SEQRES 10 X 160 GLY LYS ASP ASN SER ARG GLU TRP GLN GLU PHE LYS ALA SEQRES 11 X 160 ARG VAL GLU THR SER ARG PHE PRO ARG SER LYS LYS GLN SEQRES 12 X 160 ARG ILE LEU LEU GLN LYS PHE ASP GLU ASP GLY PHE LYS SEQRES 13 X 160 GLU ARG ASN LEU SEQRES 1 Y 86 MET ALA ASN LYS THR TYR LYS ILE GLY LYS ASN ALA GLY SEQRES 2 Y 86 TYR ASP GLY CYS GLY LEU CYS LEU ALA ALA ILE SER GLU SEQRES 3 Y 86 ASN GLU ALA ILE LYS VAL LYS TYR LEU ARG ASP ILE CYS SEQRES 4 Y 86 PRO ASP TYR ASP GLY ASP ASP LYS ALA GLU ASP TRP LEU SEQRES 5 Y 86 ARG TRP GLY THR ASP SER ARG VAL LYS ALA ALA ALA LEU SEQRES 6 Y 86 GLU MET GLU GLN TYR ALA TYR THR SER VAL GLY MET ALA SEQRES 7 Y 86 SER CYS TRP GLU PHE VAL GLU LEU FORMUL 3 HOH *140(H2 O) HELIX 1 AA1 SER X 512 PHE X 541 1 30 HELIX 2 AA2 LYS X 549 GLN X 562 1 14 HELIX 3 AA3 ASN X 574 LEU X 578 5 5 HELIX 4 AA4 PRO X 591 TRP X 596 1 6 HELIX 5 AA5 SER X 599 ASN X 601 5 3 HELIX 6 AA6 GLY X 608 GLY X 615 1 8 HELIX 7 AA7 THR X 618 PHE X 623 1 6 HELIX 8 AA8 ASN X 624 ASN X 628 5 5 HELIX 9 AA9 SER X 629 SER X 642 1 14 HELIX 10 AB1 PRO X 645 LEU X 653 1 9 HELIX 11 AB2 LEU Y 35 CYS Y 39 1 5 HELIX 12 AB3 LYS Y 47 GLU Y 49 5 3 HELIX 13 AB4 ASP Y 50 GLY Y 55 1 6 HELIX 14 AB5 ASP Y 57 GLN Y 69 1 13 SHEET 1 AA1 2 VAL X 584 HIS X 588 0 SHEET 2 AA1 2 LYS X 603 LEU X 607 -1 O VAL X 606 N GLU X 585 SHEET 1 AA2 6 THR Y 5 ILE Y 8 0 SHEET 2 AA2 6 GLU Y 28 TYR Y 34 1 O ALA Y 29 N LYS Y 7 SHEET 3 AA2 6 GLY Y 18 SER Y 25 -1 N SER Y 25 O GLU Y 28 SHEET 4 AA2 6 TYR Y 72 SER Y 79 -1 O ALA Y 78 N GLY Y 18 SHEET 5 AA2 6 GLU Y 82 GLU Y 85 -1 O VAL Y 84 N MET Y 77 SHEET 6 AA2 6 THR Y 5 ILE Y 8 -1 N TYR Y 6 O PHE Y 83 CRYST1 93.061 60.742 46.428 90.00 108.25 90.00 C 1 2 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 0.010746 0.000000 0.003543 0.00000 SCALE2 0.000000 0.016463 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022680 0.00000