HEADER ANTIMICROBIAL PROTEIN 24-MAY-22 7XVO TITLE A BACTERIA PROTEIN COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRISPR-ASSOCIATED ENDONUCLEASE CAS9; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.-.-; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 8 CHAIN: D; COMPND 9 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: HAEMOPHILUS PARAINFLUENZAE; SOURCE 9 ORGANISM_TAXID: 729; SOURCE 10 GENE: NCTC10672_00033, NCTC10672_02354; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS A BACTERIA PROTEIN COMPLEX, ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,X.Z.LI,G.Y.SONG REVDAT 1 30-AUG-23 7XVO 0 JRNL AUTH H.ZHANG,X.Z.LI,G.Y.SONG JRNL TITL A BACTERIA PROTEIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 28124 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.232 REMARK 3 R VALUE (WORKING SET) : 0.231 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1434 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 31.8000 - 4.3000 1.00 2791 127 0.2045 0.2557 REMARK 3 2 4.3000 - 3.4200 1.00 2672 159 0.2121 0.2403 REMARK 3 3 3.4100 - 2.9800 1.00 2657 159 0.2436 0.2428 REMARK 3 4 2.9800 - 2.7100 1.00 2686 131 0.2515 0.2593 REMARK 3 5 2.7100 - 2.5200 1.00 2670 147 0.2427 0.2772 REMARK 3 6 2.5200 - 2.3700 1.00 2627 154 0.2684 0.2907 REMARK 3 7 2.3700 - 2.2500 1.00 2643 151 0.2532 0.2632 REMARK 3 8 2.2500 - 2.1500 1.00 2682 108 0.2732 0.2946 REMARK 3 9 2.1500 - 2.0700 1.00 2627 152 0.2762 0.3319 REMARK 3 10 2.0700 - 2.0000 1.00 2635 146 0.3034 0.3577 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) : 0.289 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.422 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.93 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 : 0.003 2351 REMARK 3 ANGLE : 0.634 3151 REMARK 3 CHIRALITY : 0.040 348 REMARK 3 PLANARITY : 0.005 405 REMARK 3 DIHEDRAL : 4.678 308 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): -44.6059 17.1657 -1.9422 REMARK 3 T TENSOR REMARK 3 T11: 0.3749 T22: 0.2862 REMARK 3 T33: 0.3104 T12: 0.0017 REMARK 3 T13: -0.0374 T23: -0.0166 REMARK 3 L TENSOR REMARK 3 L11: 0.5525 L22: 3.0261 REMARK 3 L33: -0.0216 L12: 1.2316 REMARK 3 L13: 0.0256 L23: 0.1127 REMARK 3 S TENSOR REMARK 3 S11: -0.0761 S12: -0.0468 S13: 0.0043 REMARK 3 S21: -0.1322 S22: 0.0236 S23: -0.1173 REMARK 3 S31: -0.0347 S32: 0.2266 S33: 0.0542 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 7XVO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1300029701. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-NOV-21 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 : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28150 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 63.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.3900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 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: 6JDV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2-PROPANOL, SODIUM CITRATE TRIBASIC REMARK 280 DIHYDRATE, POLYETHYLENE GLYCOL 400, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291.15K 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 14.79467 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 29.58933 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 22.19200 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 36.98667 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 7.39733 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: 1940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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 ASP A 340 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 LYS A 312 O HOH A 501 1.95 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 ASN A 270 48.20 -87.80 REMARK 500 GLU A 290 114.91 -165.28 REMARK 500 LYS A 419 151.67 81.62 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7XVO A 249 449 UNP A0A8I1A9C6_NEIME DBREF2 7XVO A A0A8I1A9C6 249 449 DBREF1 7XVO D 1 88 UNP A0A377JKY9_HAEPA DBREF2 7XVO D A0A377JKY9 1 88 SEQADV 7XVO SER D 6 UNP A0A377JKY ALA 6 CONFLICT SEQADV 7XVO GLU D 29 UNP A0A377JKY ASN 29 CONFLICT SEQADV 7XVO LYS D 64 UNP A0A377JKY GLN 64 CONFLICT SEQRES 1 A 201 ASP ALA VAL GLN LYS MET LEU GLY HIS CYS THR PHE GLU SEQRES 2 A 201 PRO ALA GLU PRO LYS ALA ALA LYS ASN THR TYR THR ALA SEQRES 3 A 201 GLU ARG PHE ILE TRP LEU THR LYS LEU ASN ASN LEU ARG SEQRES 4 A 201 ILE LEU GLU GLN GLY SER GLU ARG PRO LEU THR ASP THR SEQRES 5 A 201 GLU ARG ALA THR LEU MET ASP GLU PRO TYR ARG LYS SER SEQRES 6 A 201 LYS LEU THR TYR ALA GLN ALA ARG LYS LEU LEU GLY LEU SEQRES 7 A 201 GLU ASP THR ALA PHE PHE LYS GLY LEU ARG TYR GLY LYS SEQRES 8 A 201 ASP ASN ALA GLU ALA SER THR LEU MET GLU MET LYS ALA SEQRES 9 A 201 TYR HIS ALA ILE SER ARG ALA LEU GLU LYS GLU GLY LEU SEQRES 10 A 201 LYS ASP LYS LYS SER PRO LEU ASN LEU SER PRO GLU LEU SEQRES 11 A 201 GLN ASP GLU ILE GLY THR ALA PHE SER LEU PHE LYS THR SEQRES 12 A 201 ASP GLU ASP ILE THR GLY ARG LEU LYS ASP ARG ILE GLN SEQRES 13 A 201 PRO GLU ILE LEU GLU ALA LEU LEU LYS HIS ILE SER PHE SEQRES 14 A 201 ASP LYS PHE VAL GLN ILE SER LEU LYS ALA LEU ARG ARG SEQRES 15 A 201 ILE VAL PRO LEU MET GLU GLN GLY LYS ARG TYR ASP GLU SEQRES 16 A 201 ALA CYS ALA GLU ILE TYR SEQRES 1 D 88 MET LYS ILE THR SER SER ASN PHE ALA THR ILE ALA THR SEQRES 2 D 88 SER GLU ASN PHE ALA LYS LEU SER VAL LEU PRO LYS ASN SEQRES 3 D 88 HIS ARG GLU PRO ILE LYS GLY LEU PHE LYS SER ALA VAL SEQRES 4 D 88 GLU GLN PHE SER SER ALA ARG ASP PHE PHE LYS ASN GLU SEQRES 5 D 88 ASN TYR SER LYS GLU LEU ALA GLU LYS PHE ASN LYS GLU SEQRES 6 D 88 ALA VAL ASN GLU ALA VAL GLU LYS LEU GLN LYS ALA ILE SEQRES 7 D 88 ASP LEU ALA GLU LYS GLN GLY ILE GLN PHE FORMUL 3 HOH *105(H2 O) HELIX 1 AA1 THR A 271 LEU A 286 1 16 HELIX 2 AA2 THR A 298 ASP A 307 1 10 HELIX 3 AA3 GLU A 308 ARG A 311 5 4 HELIX 4 AA4 TYR A 317 GLY A 325 1 9 HELIX 5 AA5 ASN A 341 ALA A 344 5 4 HELIX 6 AA6 MET A 350 GLU A 363 1 14 HELIX 7 AA7 SER A 375 PHE A 389 1 15 HELIX 8 AA8 THR A 391 LYS A 400 1 10 HELIX 9 AA9 GLN A 404 ILE A 415 1 12 HELIX 10 AB1 LEU A 425 GLN A 437 1 13 HELIX 11 AB2 ARG A 440 TYR A 449 1 10 HELIX 12 AB3 ASN D 7 ALA D 12 1 6 HELIX 13 AB4 THR D 13 LYS D 19 1 7 HELIX 14 AB5 LEU D 20 LEU D 23 5 4 HELIX 15 AB6 PRO D 24 SER D 44 1 21 HELIX 16 AB7 ARG D 46 ASN D 51 1 6 HELIX 17 AB8 SER D 55 GLN D 84 1 30 SHEET 1 AA1 2 LYS A 266 ALA A 268 0 SHEET 2 AA1 2 PHE A 420 SER A 424 -1 O ILE A 423 N ALA A 267 SHEET 1 AA2 3 SER A 293 PRO A 296 0 SHEET 2 AA2 3 ARG A 287 GLU A 290 -1 N ILE A 288 O ARG A 295 SHEET 3 AA2 3 PHE A 331 PHE A 332 -1 O PHE A 331 N LEU A 289 SHEET 1 AA3 2 LEU A 315 THR A 316 0 SHEET 2 AA3 2 THR A 346 MET A 348 -1 O LEU A 347 N LEU A 315 CRYST1 127.210 127.210 44.384 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 0.007861 0.004539 0.000000 0.00000 SCALE2 0.000000 0.009077 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022531 0.00000