HEADER ANTIMICROBIAL PROTEIN 08-DEC-22 8HNS TITLE CRYSTAL STRUCTURE OF AN ANTI-CRISPR PROTEIN ACRIIC4 IN APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-CRISPR PROTEIN ACRIIC4; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: WP_049372635.1;THE FIRST RESIDUE 'SER' OF THE SAMPLE COMPND 6 SEQUENCE IS THE ONE EXPRESSED FROM THE VECTOR LEFT AFTER TAG COMPND 7 CLEAVAGE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS PARAINFLUENZAE; SOURCE 3 ORGANISM_TAXID: 729; SOURCE 4 GENE: ACRIIC4; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ANTI-CRISPR PROTEIN, CLEAVAGE INHIBITION, DIMER, ANTIMICROBIAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR W.SUN,Z.CHENG,J.YANG,Y.WANG REVDAT 3 29-MAY-24 8HNS 1 REMARK REVDAT 2 02-AUG-23 8HNS 1 JRNL REVDAT 1 19-JUL-23 8HNS 0 JRNL AUTH W.SUN,Z.CHENG,J.WANG,J.YANG,X.LI,J.WANG,M.CHEN,X.YANG, JRNL AUTH 2 G.SHENG,J.LOU,Y.WANG JRNL TITL ACRIIC4 INHIBITS TYPE II-C CAS9 BY PREVENTING R-LOOP JRNL TITL 2 FORMATION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 75120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 37494395 JRNL DOI 10.1073/PNAS.2303675120 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.LEE,A.MIR,A.EDRAKI,B.GARCIA,N.AMRANI,H.E.LOU, REMARK 1 AUTH 2 I.GAINETDINOV,A.PAWLUK,R.IBRAHEIM,X.D.GAO,P.LIU, REMARK 1 AUTH 3 A.R.DAVIDSON,K.L.MAXWELL,E.J.SONTHEIMER REMARK 1 TITL POTENT CAS9 INHIBITION IN BACTERIAL AND HUMAN CELLS BY REMARK 1 TITL 2 ACRIIC4 AND ACRIIC5 ANTI-CRISPR PROTEINS. REMARK 1 REF MBIO V. 9 2018 REMARK 1 REFN ESSN 2150-7511 REMARK 1 DOI 10.1128/MBIO.02321-18 REMARK 2 REMARK 2 RESOLUTION. 2.54 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 2.54 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.20 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 6302 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 296 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 37.2000 - 3.2000 0.99 3186 140 0.1954 0.2232 REMARK 3 2 3.2000 - 2.5400 0.92 2820 156 0.2816 0.2801 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) : 22.618 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 32.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.51 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 : 0.021 1430 REMARK 3 ANGLE : 1.418 1910 REMARK 3 CHIRALITY : 0.108 208 REMARK 3 PLANARITY : 0.008 248 REMARK 3 DIHEDRAL : 27.824 540 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 8HNS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1300033995. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-18 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 : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6556 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.540 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 37.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.54 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.58 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.83000 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: AUTOSOL REMARK 200 STARTING MODEL: IN-HOUSE MODEL ( THE CRYSTAL STRUCTURE OF A SEMET REMARK 200 -DERIVATIVE OF THIS PROTEIN USING SAD) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS, SODIUM CHLORIDE, SODIUM ACETATE, REMARK 280 PEG 3350, GLYCEROL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 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 -Y,X,Z REMARK 290 4555 Y,-X,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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 83.17900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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: 4670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11120 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 83.17900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 SER A 0 REMARK 465 SER B 0 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 A 50 CG CD CE NZ REMARK 470 LYS B 50 CG CD CE NZ 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 214 DISTANCE = 6.29 ANGSTROMS DBREF 8HNS A 0 88 PDB 8HNS 8HNS 0 88 DBREF 8HNS B 0 88 PDB 8HNS 8HNS 0 88 SEQRES 1 A 89 SER MET LYS ILE THR SER SER ASN PHE ALA THR ILE ALA SEQRES 2 A 89 THR SER GLU ASN PHE ALA LYS LEU SER VAL LEU PRO LYS SEQRES 3 A 89 ASN HIS ARG GLU PRO ILE LYS GLY LEU PHE LYS SER ALA SEQRES 4 A 89 VAL GLU GLN PHE SER SER ALA ARG ASP PHE PHE LYS ASN SEQRES 5 A 89 GLU ASN TYR SER LYS GLU LEU ALA GLU LYS PHE ASN LYS SEQRES 6 A 89 GLU ALA VAL ASN GLU ALA VAL GLU LYS LEU GLN LYS ALA SEQRES 7 A 89 ILE ASP LEU ALA GLU LYS GLN GLY ILE GLN PHE SEQRES 1 B 89 SER MET LYS ILE THR SER SER ASN PHE ALA THR ILE ALA SEQRES 2 B 89 THR SER GLU ASN PHE ALA LYS LEU SER VAL LEU PRO LYS SEQRES 3 B 89 ASN HIS ARG GLU PRO ILE LYS GLY LEU PHE LYS SER ALA SEQRES 4 B 89 VAL GLU GLN PHE SER SER ALA ARG ASP PHE PHE LYS ASN SEQRES 5 B 89 GLU ASN TYR SER LYS GLU LEU ALA GLU LYS PHE ASN LYS SEQRES 6 B 89 GLU ALA VAL ASN GLU ALA VAL GLU LYS LEU GLN LYS ALA SEQRES 7 B 89 ILE ASP LEU ALA GLU LYS GLN GLY ILE GLN PHE HET GOL A 101 6 HET GOL B 101 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *24(H2 O) HELIX 1 AA1 ASN A 7 ALA A 12 1 6 HELIX 2 AA2 THR A 13 LEU A 20 1 8 HELIX 3 AA3 SER A 21 LEU A 23 5 3 HELIX 4 AA4 PRO A 24 LYS A 83 1 60 HELIX 5 AA5 ASN B 7 ALA B 12 1 6 HELIX 6 AA6 THR B 13 LYS B 19 1 7 HELIX 7 AA7 LEU B 20 LEU B 23 5 4 HELIX 8 AA8 PRO B 24 GLN B 84 1 61 CRYST1 83.179 83.179 27.814 90.00 90.00 90.00 P 4 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 0.012022 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012022 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035953 0.00000