HEADER VIRAL PROTEIN 10-DEC-18 6Q67 TITLE CRYSTAL STRUCTURE OF PORCINE ACBD3 GOLD DOMAIN IN COMPLEX WITH 3A TITLE 2 PROTEIN OF AICHIVIRUS C COMPND MOL_ID: 1; COMPND 2 MOLECULE: PERIPHERIAL BENZODIAZEPINE RECEPTOR ASSOCIATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 3A; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA; SOURCE 3 ORGANISM_COMMON: PIG; SOURCE 4 ORGANISM_TAXID: 9823; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: AICHIVIRUS C; SOURCE 9 ORGANISM_TAXID: 1298633; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS COMPLEX, AICHIVIRUS, PICORNAVIRUS, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.SMOLA,E.BOURA,M.KLIMA REVDAT 5 24-JAN-24 6Q67 1 HETSYN REVDAT 4 29-JUL-20 6Q67 1 COMPND REMARK HETNAM SITE REVDAT 3 12-FEB-20 6Q67 1 JRNL REVDAT 2 25-DEC-19 6Q67 1 JRNL REVDAT 1 13-NOV-19 6Q67 0 JRNL AUTH M.SMOLA,V.HOROVA,E.BOURA,M.KLIMA JRNL TITL STRUCTURAL BASIS FOR HIJACKING OF THE HOST ACBD3 PROTEIN BY JRNL TITL 2 BOVINE AND PORCINE ENTEROVIRUSES AND KOBUVIRUSES. JRNL REF ARCH. VIROL. V. 165 355 2020 JRNL REFN ISSN 1432-8798 JRNL PMID 31845156 JRNL DOI 10.1007/S00705-019-04490-9 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 14902 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 746 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 47.9800 - 3.8444 1.00 3012 159 0.1897 0.2199 REMARK 3 2 3.8444 - 3.0516 0.99 2844 149 0.2724 0.3258 REMARK 3 3 3.0516 - 2.6659 0.99 2774 145 0.3009 0.3172 REMARK 3 4 2.6659 - 2.4222 0.98 2781 148 0.3296 0.3375 REMARK 3 5 2.4222 - 2.2486 0.98 2745 145 0.3841 0.4514 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.420 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 68.26 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 79.00 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 1301 REMARK 3 ANGLE : 1.144 1774 REMARK 3 CHIRALITY : 0.041 192 REMARK 3 PLANARITY : 0.008 224 REMARK 3 DIHEDRAL : 14.417 458 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 6Q67 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1200013339. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-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 : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS JAN 26, 2018 REMARK 200 DATA SCALING SOFTWARE : XDS JAN 26, 2018 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14951 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.249 REMARK 200 RESOLUTION RANGE LOW (A) : 47.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : 0.03611 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.4900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 1.23200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.010 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.6 REMARK 200 STARTING MODEL: 5LZ1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% W/V PEG 3000, 10% V/V 1,4 REMARK 280 -BUTANEDIOL, 1% W/V N,N-DIMETHYLDODECYLAMINE-N-OXIDE , 10% W/V REMARK 280 GLUCOSE, 20MM L-ARGININE, 20MM L-THREONINE, 20MM L-HISTIDINE, REMARK 280 20MM BETAINE, 10MM TRANS-4-HYDROXY-L-PROLINE, 100MM BES/TEA PH REMARK 280 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 56.51333 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 113.02667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 113.02667 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 56.51333 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: 2410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 363 REMARK 465 GLU A 364 REMARK 465 SER A 365 REMARK 465 LEU A 366 REMARK 465 ASP A 437 REMARK 465 SER A 438 REMARK 465 PRO A 439 REMARK 465 ASN A 440 REMARK 465 THR A 441 REMARK 465 ALA A 442 REMARK 465 VAL A 443 REMARK 465 SER A 444 REMARK 465 VAL A 445 REMARK 465 HIS A 446 REMARK 465 VAL A 447 REMARK 465 SER A 448 REMARK 465 GLU A 449 REMARK 465 SER A 450 REMARK 465 SER A 451 REMARK 465 GLU A 452 REMARK 465 HIS A 453 REMARK 465 ASP A 454 REMARK 465 ASP A 455 REMARK 465 GLU A 456 REMARK 465 GLU A 457 REMARK 465 GLU A 458 REMARK 465 GLU A 459 REMARK 465 GLU A 460 REMARK 465 ASN A 461 REMARK 465 ILE A 462 REMARK 465 SER A 463 REMARK 465 SER A 464 REMARK 465 GLU A 465 REMARK 465 GLU A 466 REMARK 465 LYS A 467 REMARK 465 ALA A 468 REMARK 465 LYS A 469 REMARK 465 LYS A 470 REMARK 465 ASN A 471 REMARK 465 ALA A 472 REMARK 465 ASN A 473 REMARK 465 THR B 29 REMARK 465 LEU B 30 REMARK 465 SER B 31 REMARK 465 PHE B 32 REMARK 465 GLU B 33 REMARK 465 ARG B 34 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 ARG A 381 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 386 CG CD CE NZ REMARK 470 LYS A 474 CG CD CE NZ REMARK 470 LYS B 24 CG CD CE NZ 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 424 15.46 58.67 REMARK 500 REMARK 500 REMARK: NULL DBREF 6Q67 A 364 529 UNP Q6DUB6 Q6DUB6_PIG 207 372 DBREF 6Q67 B 1 34 PDB 6Q67 6Q67 1 34 SEQADV 6Q67 MET A 363 UNP Q6DUB6 INITIATING METHIONINE SEQRES 1 A 167 MET GLU SER LEU PRO VAL ILE ALA ALA PRO SER MET TRP SEQRES 2 A 167 THR ARG PRO GLN ILE ARG ASP PHE LYS GLU LYS ILE ARG SEQRES 3 A 167 GLN ASP SER ASP SER VAL ILE THR VAL GLY ARG GLY GLU SEQRES 4 A 167 VAL VAL THR VAL ARG VAL PRO THR HIS GLU GLU GLY SER SEQRES 5 A 167 TYR LEU PHE TRP GLU PHE ALA THR ASP ASN TYR ASP ILE SEQRES 6 A 167 GLY PHE GLY VAL TYR PHE GLU TRP THR ASP SER PRO ASN SEQRES 7 A 167 THR ALA VAL SER VAL HIS VAL SER GLU SER SER GLU HIS SEQRES 8 A 167 ASP ASP GLU GLU GLU GLU GLU ASN ILE SER SER GLU GLU SEQRES 9 A 167 LYS ALA LYS LYS ASN ALA ASN LYS PRO VAL LEU ASP GLU SEQRES 10 A 167 ILE VAL PRO VAL TYR ARG ARG ASP CYS HIS GLU GLU VAL SEQRES 11 A 167 TYR ALA GLY SER HIS GLN TYR PRO GLY ARG GLY VAL TYR SEQRES 12 A 167 LEU LEU LYS PHE ASP ASN SER TYR SER LEU TRP ARG SER SEQRES 13 A 167 LYS SER VAL TYR TYR ARG VAL TYR TYR THR ARG SEQRES 1 B 34 GLY LEU THR ILE GLU ALA GLU PRO THR GLU LEU SER TYR SEQRES 2 B 34 GLN ASP ALA LEU GLU MET LEU ALA GLU SER LYS PRO VAL SEQRES 3 B 34 SER THR THR LEU SER PHE GLU ARG HET BGC A 601 12 HETNAM BGC BETA-D-GLUCOPYRANOSE HETSYN BGC BETA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 3 BGC C6 H12 O6 HELIX 1 AA1 GLN A 379 GLN A 389 1 11 HELIX 2 AA2 ASP A 390 ASP A 392 5 3 HELIX 3 AA3 SER B 12 ALA B 21 1 10 SHEET 1 AA1 3 VAL A 394 VAL A 397 0 SHEET 2 AA1 3 LYS A 519 THR A 528 -1 O LYS A 519 N VAL A 397 SHEET 3 AA1 3 THR B 9 GLU B 10 1 O THR B 9 N TYR A 527 SHEET 1 AA2 6 VAL A 394 VAL A 397 0 SHEET 2 AA2 6 LYS A 519 THR A 528 -1 O LYS A 519 N VAL A 397 SHEET 3 AA2 6 TYR A 415 THR A 422 -1 N PHE A 417 O TYR A 526 SHEET 4 AA2 6 VAL A 492 GLN A 498 -1 O TYR A 493 N PHE A 420 SHEET 5 AA2 6 SER A 373 ARG A 377 -1 N SER A 373 O SER A 496 SHEET 6 AA2 6 LYS B 24 VAL B 26 -1 O LYS B 24 N THR A 376 SHEET 1 AA3 5 LEU A 477 ARG A 486 0 SHEET 2 AA3 5 ILE A 427 TRP A 435 -1 N VAL A 431 O VAL A 481 SHEET 3 AA3 5 GLY A 503 ASP A 510 -1 O VAL A 504 N GLU A 434 SHEET 4 AA3 5 VAL A 402 PRO A 408 -1 N VAL A 407 O TYR A 505 SHEET 5 AA3 5 THR B 3 GLU B 5 1 O ILE B 4 N ARG A 406 CRYST1 55.390 55.390 169.540 90.00 90.00 120.00 P 31 2 1 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 0.018054 0.010423 0.000000 0.00000 SCALE2 0.000000 0.020847 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005898 0.00000