PDB Short entry for 5LZ1 HEADER SIGNALING PROTEIN 29-SEP-16 5LZ1 TITLE CRYSTAL STRUCTURE OF HUMAN ACBD3 GOLD DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GOLGI RESIDENT PROTEIN GCP60; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ACYL-COA-BINDING DOMAIN-CONTAINING PROTEIN 3,GOLGI COMPLEX- COMPND 5 ASSOCIATED PROTEIN 1,GOCAP1,GOLGI PHOSPHOPROTEIN 1,GOLPH1,PBR- AND COMPND 6 PKA-ASSOCIATED PROTEIN 7,PERIPHERAL BENZODIAZEPINE RECEPTOR- COMPND 7 ASSOCIATED PROTEIN PAP7; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ACBD3, GCP60, GOCAP1, GOLPH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS ACBD3, GOLD, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.KLIMA,E.BOURA REVDAT 3 17-JAN-24 5LZ1 1 REMARK REVDAT 2 13-DEC-17 5LZ1 1 JRNL REVDAT 1 14-DEC-16 5LZ1 0 JRNL AUTH M.KLIMA,D.CHALUPSKA,B.ROZYCKI,J.HUMPOLICKOVA,L.REZABKOVA, JRNL AUTH 2 J.SILHAN,A.BAUMLOVA,A.DUBANKOVA,E.BOURA JRNL TITL KOBUVIRAL NON-STRUCTURAL 3A PROTEINS ACT AS MOLECULAR JRNL TITL 2 HARNESSES TO HIJACK THE HOST ACBD3 PROTEIN. JRNL REF STRUCTURE V. 25 219 2017 JRNL REFN ISSN 1878-4186 JRNL PMID 28065508 JRNL DOI 10.1016/J.STR.2016.11.021 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 18575 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 930 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 39.7543 - 3.8250 1.00 2711 143 0.1854 0.2026 REMARK 3 2 3.8250 - 3.0364 1.00 2553 135 0.2118 0.2274 REMARK 3 3 3.0364 - 2.6526 1.00 2504 132 0.2469 0.3086 REMARK 3 4 2.6526 - 2.4101 1.00 2489 131 0.2645 0.3160 REMARK 3 5 2.4101 - 2.2374 1.00 2487 130 0.2703 0.3417 REMARK 3 6 2.2374 - 2.1055 1.00 2460 130 0.2918 0.3004 REMARK 3 7 2.1055 - 2.0001 1.00 2441 129 0.3017 0.3566 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.89 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 : 0.003 1184 REMARK 3 ANGLE : 0.896 1617 REMARK 3 CHIRALITY : 0.035 171 REMARK 3 PLANARITY : 0.004 206 REMARK 3 DIHEDRAL : 12.549 415 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 5LZ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1200001616. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-14 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) : 1.282724 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 VERSION OCT 15, 2015 REMARK 200 DATA SCALING SOFTWARE : XDS VERSION OCT 15, 2015 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18582 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 39.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.05942 REMARK 200 R SYM (I) : 0.05942 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.6600 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 1.34900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.430 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: 1OLM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS PH 8.8, 25% W/V PEG 3.350, REMARK 280 20% GLYCEROL, 20MM 2-PROPANOL/1,2 -PROPANEDIOL/1,3-PROPANEDIOL/1- REMARK 280 BUTANOL/1,4-BUTANEDIOL/1,6-HEXANEDIOL, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 81.96000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.10500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.10500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 122.94000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.10500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.10500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 40.98000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.10500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.10500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 122.94000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.10500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.10500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 40.98000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 81.96000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7940 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 GLY A 361 REMARK 465 ALA A 362 REMARK 465 MET A 363 REMARK 465 GLU A 449 REMARK 465 SER A 450 REMARK 465 SER A 451 REMARK 465 ASP A 452 REMARK 465 ASP A 453 REMARK 465 ASP A 454 REMARK 465 GLU A 455 REMARK 465 GLU A 456 REMARK 465 GLU A 457 REMARK 465 GLU A 458 REMARK 465 GLU A 459 REMARK 465 ASN A 460 REMARK 465 ILE A 461 REMARK 465 GLY A 462 REMARK 465 CYS A 463 REMARK 465 GLU A 464 REMARK 465 GLU A 465 REMARK 465 LYS A 466 REMARK 465 ALA A 467 REMARK 465 LYS A 468 REMARK 465 LYS A 469 REMARK 465 ASN A 470 REMARK 465 ALA A 471 REMARK 465 ASN A 472 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 381 CG CD CE NZ REMARK 470 GLU A 411 CG CD OE1 OE2 REMARK 470 GLU A 412 CG CD OE1 OE2 REMARK 470 LYS A 473 CG CD CE NZ 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 601 O HOH A 603 2.16 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 ASP A 423 -60.46 -91.92 REMARK 500 REMARK 500 REMARK: NULL DBREF 5LZ1 A 364 528 UNP Q9H3P7 GCP60_HUMAN 364 528 SEQADV 5LZ1 GLY A 361 UNP Q9H3P7 EXPRESSION TAG SEQADV 5LZ1 ALA A 362 UNP Q9H3P7 EXPRESSION TAG SEQADV 5LZ1 MET A 363 UNP Q9H3P7 EXPRESSION TAG SEQRES 1 A 168 GLY ALA MET GLU SER LEU PRO VAL ILE ALA ALA PRO SER SEQRES 2 A 168 MET TRP THR ARG PRO GLN ILE LYS ASP PHE LYS GLU LYS SEQRES 3 A 168 ILE GLN GLN ASP ALA ASP SER VAL ILE THR VAL GLY ARG SEQRES 4 A 168 GLY GLU VAL VAL THR VAL ARG VAL PRO THR HIS GLU GLU SEQRES 5 A 168 GLY SER TYR LEU PHE TRP GLU PHE ALA THR ASP ASN TYR SEQRES 6 A 168 ASP ILE GLY PHE GLY VAL TYR PHE GLU TRP THR ASP SER SEQRES 7 A 168 PRO ASN THR ALA VAL SER VAL HIS VAL SER GLU SER SER SEQRES 8 A 168 ASP ASP ASP GLU GLU GLU GLU GLU ASN ILE GLY CYS GLU SEQRES 9 A 168 GLU LYS ALA LYS LYS ASN ALA ASN LYS PRO LEU LEU ASP SEQRES 10 A 168 GLU ILE VAL PRO VAL TYR ARG ARG ASP CYS HIS GLU GLU SEQRES 11 A 168 VAL TYR ALA GLY SER HIS GLN TYR PRO GLY ARG GLY VAL SEQRES 12 A 168 TYR LEU LEU LYS PHE ASP ASN SER TYR SER LEU TRP ARG SEQRES 13 A 168 SER LYS SER VAL TYR TYR ARG VAL TYR TYR THR ARG FORMUL 2 HOH *24(H2 O) HELIX 1 AA1 GLN A 379 GLN A 388 1 10 HELIX 2 AA2 GLN A 389 ASP A 392 5 4 SHEET 1 AA1 5 SER A 373 ARG A 377 0 SHEET 2 AA1 5 VAL A 491 GLN A 497 -1 O VAL A 491 N ARG A 377 SHEET 3 AA1 5 TYR A 415 ALA A 421 -1 N PHE A 420 O TYR A 492 SHEET 4 AA1 5 LYS A 518 THR A 527 -1 O TYR A 521 N ALA A 421 SHEET 5 AA1 5 VAL A 394 VAL A 397 -1 N ILE A 395 O VAL A 520 SHEET 1 AA2 5 SER A 444 SER A 448 0 SHEET 2 AA2 5 VAL A 402 PRO A 408 -1 N THR A 404 O HIS A 446 SHEET 3 AA2 5 VAL A 503 ASP A 509 -1 O PHE A 508 N VAL A 403 SHEET 4 AA2 5 ILE A 427 GLU A 434 -1 N TYR A 432 O LEU A 505 SHEET 5 AA2 5 LEU A 476 ARG A 485 -1 O ASP A 477 N PHE A 433 CRYST1 56.210 56.210 163.920 90.00 90.00 90.00 P 43 21 2 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 0.017790 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017790 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006101 0.00000