HEADER IMMUNE SYSTEM 14-JUL-22 7YHR TITLE ANTI-CRISPR PROTEIN ACRIC5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANTI-CRISPR PROTEIN TYPE I-C5; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS DELHIENSIS; SOURCE 3 ORGANISM_TAXID: 366289; SOURCE 4 GENE: SAMN05216189_103750; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ACRIC5, IMMUNE SYSTEM, INHIBITOR, ANTI-CRISPR EXPDTA X-RAY DIFFRACTION AUTHOR Y.J.KANG,H.H.PARK REVDAT 3 05-JUN-24 7YHR 1 JRNL REVDAT 2 29-NOV-23 7YHR 1 REMARK REVDAT 1 24-MAY-23 7YHR 0 JRNL AUTH Y.J.KANG,H.H.PARK JRNL TITL HIGH-RESOLUTION CRYSTAL STRUCTURE OF THE ANTI-CRISPR PROTEIN JRNL TITL 2 ACRIC5. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 625 102 2022 JRNL REFN ESSN 1090-2104 JRNL PMID 35952606 JRNL DOI 10.1016/J.BBRC.2022.08.005 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17_3644 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.49 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 12799 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 641 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 23.4900 - 2.4800 1.00 2464 130 0.1914 0.2117 REMARK 3 2 2.4800 - 1.9700 1.00 2439 129 0.2172 0.2301 REMARK 3 3 1.9700 - 1.7200 1.00 2422 127 0.2251 0.2373 REMARK 3 4 1.7200 - 1.5600 1.00 2418 128 0.2422 0.3019 REMARK 3 5 1.5600 - 1.4500 1.00 2415 127 0.3283 0.3673 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) : 0.186 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.722 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.72 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 : 0.007 479 REMARK 3 ANGLE : 0.821 648 REMARK 3 CHIRALITY : 0.067 69 REMARK 3 PLANARITY : 0.006 89 REMARK 3 DIHEDRAL : 4.912 60 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 7YHR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300030944. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-21 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 : 12804 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 23.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 20.40 REMARK 200 R MERGE (I) : 0.08486 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 2.24800 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: 5GM6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M SODIUM CITRATE TRIBASIC REMARK 280 DIGYDRATE PH6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 14.27667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.55333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.41500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.69167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 7.13833 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 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 122 O HOH A 150 2.14 REMARK 500 OD2 ASP A 53 O HOH A 101 2.15 REMARK 500 OE2 GLU A 27 O HOH A 102 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 A 110 O HOH A 136 5554 1.86 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7YHR A 1 60 UNP A0A239N0M2_9PSED DBREF2 7YHR A A0A239N0M2 1 60 SEQRES 1 A 60 MET SER LYS VAL THR LEU ASN GLY GLN GLN ILE ASP PHE SEQRES 2 A 60 ASP ALA ALA VAL ASN LEU MET ASP ALA GLU LEU ARG GLU SEQRES 3 A 60 GLU LEU HIS SER ALA GLN GLU TRP THR ASN ASP GLN GLU SEQRES 4 A 60 PHE LEU ASP ALA TYR VAL GLN ALA HIS ALA ALA LYS PHE SEQRES 5 A 60 ASP GLY GLU GLU PHE GLN VAL ALA FORMUL 2 HOH *53(H2 O) HELIX 1 AA1 PHE A 13 MET A 20 1 8 HELIX 2 AA2 ASP A 21 GLN A 32 1 12 HELIX 3 AA3 ASN A 36 PHE A 52 1 17 SHEET 1 AA1 2 LYS A 3 LEU A 6 0 SHEET 2 AA1 2 GLN A 9 ASP A 12 -1 O ILE A 11 N VAL A 4 CRYST1 54.250 54.250 42.830 90.00 90.00 120.00 P 61 6 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 0.018433 0.010642 0.000000 0.00000 SCALE2 0.000000 0.021285 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023348 0.00000 TER 472 ALA A 60 HETATM 473 O HOH A 101 16.650 32.532 3.652 1.00 45.01 O HETATM 474 O HOH A 102 14.629 25.305 22.941 1.00 29.37 O HETATM 475 O HOH A 103 9.505 10.995 14.587 1.00 34.71 O HETATM 476 O HOH A 104 19.122 23.481 13.603 1.00 39.86 O HETATM 477 O HOH A 105 15.018 31.584 9.979 1.00 35.33 O HETATM 478 O HOH A 106 15.904 23.805 15.261 1.00 36.89 O HETATM 479 O HOH A 107 -5.696 24.371 4.347 1.00 37.57 O HETATM 480 O HOH A 108 12.351 12.812 15.911 1.00 25.64 O HETATM 481 O HOH A 109 -3.692 27.247 21.009 1.00 30.39 O HETATM 482 O HOH A 110 19.395 17.799 15.363 1.00 50.66 O HETATM 483 O HOH A 111 2.493 10.933 13.410 1.00 31.92 O HETATM 484 O HOH A 112 1.881 29.481 20.282 1.00 31.54 O HETATM 485 O HOH A 113 -5.782 28.086 18.133 1.00 31.37 O HETATM 486 O HOH A 114 -5.905 11.863 19.865 1.00 33.84 O HETATM 487 O HOH A 115 9.293 24.684 30.609 1.00 42.12 O HETATM 488 O HOH A 116 -5.597 17.703 4.627 1.00 48.32 O HETATM 489 O HOH A 117 6.964 28.550 18.873 1.00 29.53 O HETATM 490 O HOH A 118 -8.340 12.368 13.393 1.00 26.83 O HETATM 491 O HOH A 119 -4.172 27.075 14.076 1.00 29.56 O HETATM 492 O HOH A 120 14.957 18.320 11.657 1.00 23.51 O HETATM 493 O HOH A 121 0.613 29.848 15.762 1.00 28.25 O HETATM 494 O HOH A 122 0.363 17.475 22.456 1.00 32.98 O HETATM 495 O HOH A 123 7.965 20.452 7.982 1.00 28.05 O HETATM 496 O HOH A 124 -4.417 12.312 15.628 1.00 24.38 O HETATM 497 O HOH A 125 4.717 28.474 9.924 1.00 27.34 O HETATM 498 O HOH A 126 7.977 15.305 13.491 1.00 26.85 O HETATM 499 O HOH A 127 -4.698 9.243 13.851 1.00 38.11 O HETATM 500 O HOH A 128 6.126 27.156 28.865 1.00 37.31 O HETATM 501 O HOH A 129 0.717 27.557 21.571 1.00 25.38 O HETATM 502 O HOH A 130 -9.041 22.137 1.309 1.00 27.78 O HETATM 503 O HOH A 131 7.430 32.971 13.826 1.00 32.75 O HETATM 504 O HOH A 132 1.190 13.057 7.268 1.00 30.51 O HETATM 505 O HOH A 133 -8.094 22.450 26.486 1.00 28.05 O HETATM 506 O HOH A 134 -3.714 28.201 11.935 1.00 30.38 O HETATM 507 O HOH A 135 2.658 27.239 26.052 1.00 30.36 O HETATM 508 O HOH A 136 -5.890 25.614 24.352 1.00 37.78 O HETATM 509 O HOH A 137 -6.156 15.360 8.085 1.00 31.88 O HETATM 510 O HOH A 138 -4.613 22.614 7.088 1.00 31.49 O HETATM 511 O HOH A 139 17.123 26.530 9.219 1.00 32.60 O HETATM 512 O HOH A 140 -2.581 23.851 5.841 1.00 33.52 O HETATM 513 O HOH A 141 -3.777 31.001 9.297 1.00 38.71 O HETATM 514 O HOH A 142 4.903 23.385 4.970 1.00 36.55 O HETATM 515 O HOH A 143 -1.061 29.036 11.236 1.00 31.95 O HETATM 516 O HOH A 144 14.835 17.675 21.869 1.00 28.77 O HETATM 517 O HOH A 145 -1.368 34.061 7.562 1.00 32.42 O HETATM 518 O HOH A 146 -2.899 16.092 24.792 1.00 38.44 O HETATM 519 O HOH A 147 -0.144 29.768 -0.011 1.00 33.40 O HETATM 520 O HOH A 148 6.598 21.028 5.848 1.00 36.84 O HETATM 521 O HOH A 149 -8.103 25.291 26.950 1.00 35.33 O HETATM 522 O HOH A 150 2.252 16.488 22.282 1.00 41.28 O HETATM 523 O HOH A 151 -0.846 31.307 11.198 1.00 36.61 O HETATM 524 O HOH A 152 -5.181 12.380 7.619 1.00 42.38 O HETATM 525 O HOH A 153 -3.578 10.810 7.455 1.00 46.09 O MASTER 239 0 0 3 2 0 0 6 524 1 0 5 END