HEADER IMMUNE SYSTEM 19-JUL-23 8K4M TITLE ANTI CRISPR PROTEIN, ACRIIA13B COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI CRISPR PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS HAEMOLYTICUS; SOURCE 3 ORGANISM_TAXID: 1283; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ACRIIA13, ACRIIA13B, IMMUNE SYSTEM, CRISPR-CAS SYSTEM, CAS9, KEYWDS 2 INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR S.Y.LEE,H.H.PARK REVDAT 1 24-JUL-24 8K4M 0 JRNL AUTH S.Y.LEE,H.H.PARK JRNL TITL STRUCTURE OF ACRIIA13B AT 1.53 ANGSTROMS RESOLUTION. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.1_4122: ???) 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) : 1.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 19704 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 (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 987 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 26.4900 - 2.9300 0.94 2747 145 0.1798 0.1930 REMARK 3 2 2.9300 - 2.3200 0.96 2724 143 0.2322 0.2604 REMARK 3 3 2.3200 - 2.0300 0.96 2723 144 0.2190 0.2422 REMARK 3 4 2.0300 - 1.8400 0.92 2603 137 0.2502 0.2993 REMARK 3 5 1.8400 - 1.7100 0.94 2642 139 0.2745 0.3121 REMARK 3 6 1.7100 - 1.6100 0.94 2632 139 0.3061 0.3689 REMARK 3 7 1.6100 - 1.5300 0.93 2646 140 0.4141 0.4508 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.850 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 : 0.008 1053 REMARK 3 ANGLE : 0.994 1422 REMARK 3 CHIRALITY : 0.061 154 REMARK 3 PLANARITY : 0.006 182 REMARK 3 DIHEDRAL : 6.038 135 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 8K4M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JUL-23. REMARK 100 THE DEPOSITION ID IS D_1300039235. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-22 REMARK 200 TEMPERATURE (KELVIN) : 125 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 5C (4A) 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19723 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.530 REMARK 200 RESOLUTION RANGE LOW (A) : 26.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.8200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.59 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.2M SODIUM CITRATE PH6.1, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.15K 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 51.25500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.73500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 51.25500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.73500 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: 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 MET A 1 REMARK 465 ASN A 2 REMARK 465 GLU A 3 REMARK 465 LEU A 4 REMARK 465 ASN A 5 REMARK 465 ASN A 6 REMARK 465 GLU A 131 REMARK 465 HIS A 132 REMARK 465 HIS A 133 REMARK 465 HIS A 134 REMARK 465 HIS A 135 REMARK 465 HIS A 136 REMARK 465 HIS A 137 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 OE2 GLU A 94 O HOH A 201 2.00 REMARK 500 O HOH A 249 O HOH A 260 2.18 REMARK 500 O HOH A 245 O HOH A 256 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 TYR A 34 -55.88 -140.00 REMARK 500 REMARK 500 REMARK: NULL DBREF 8K4M A 1 137 PDB 8K4M 8K4M 1 137 SEQRES 1 A 137 MET ASN GLU LEU ASN ASN LYS MET ILE GLU ASP VAL VAL SEQRES 2 A 137 LEU GLY GLU VAL GLU LEU ILE GLU ASP LEU GLY GLN TYR SEQRES 3 A 137 PHE ILE ASP ILE GLU GLY ASP TYR GLU TYR ASN VAL GLU SEQRES 4 A 137 PHE ALA THR LEU SER GLU VAL ASP TYR LYS VAL CYS ALA SEQRES 5 A 137 LEU TYR GLU VAL ALA THR SER LYS THR TYR GLU VAL PRO SEQRES 6 A 137 TYR HIS ASP LYS LEU GLU LYS GLU ASP MET LYS LEU PHE SEQRES 7 A 137 TYR ASP LYS TRP LEU GLU LYS ASP GLN GLN GLU GLU THR SEQRES 8 A 137 TYR ILE GLU SER VAL PHE PHE VAL ASN ARG GLU ASP ALA SEQRES 9 A 137 GLU SER TYR ILE LYS ASP VAL LEU LYS GLY LYS GLU SER SEQRES 10 A 137 LEU THR GLU VAL ALA ALA GLU ILE GLY TYR PHE GLU LEU SEQRES 11 A 137 GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *91(H2 O) HELIX 1 AA1 GLU A 71 GLU A 73 5 3 HELIX 2 AA2 ASP A 74 GLU A 89 1 16 HELIX 3 AA3 ASN A 100 VAL A 111 1 12 HELIX 4 AA4 SER A 117 GLY A 126 1 10 SHEET 1 AA1 4 VAL A 17 GLY A 32 0 SHEET 2 AA1 4 TYR A 36 TYR A 48 -1 O LEU A 43 N LEU A 23 SHEET 3 AA1 4 ALA A 52 VAL A 64 -1 O VAL A 64 N TYR A 36 SHEET 4 AA1 4 TYR A 92 PHE A 98 -1 O GLU A 94 N THR A 58 CRYST1 102.510 37.470 37.090 90.00 103.29 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 0.009755 0.000000 0.002304 0.00000 SCALE2 0.000000 0.026688 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027703 0.00000