HEADER CHAPERONE 27-MAR-19 6JPT TITLE CRYSTAL STRUCTURE OF HUMAN PAC3 HOMODIMER (TRIGONAL FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEASOME ASSEMBLY CHAPERONE 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HPAC3; COMPND 5 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: PSMG3, C7ORF48, PAC3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRSF-DUET I KEYWDS PROTEASOME ASSEMBLY CHAPERONE, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR T.SATOH,M.YAGI-UTSUMI,K.OKAMOTO,E.KURIMOTO,K.TANAKA,K.KATO REVDAT 2 22-NOV-23 6JPT 1 LINK REVDAT 1 29-MAY-19 6JPT 0 JRNL AUTH T.SATOH,M.YAGI-UTSUMI,K.OKAMOTO,E.KURIMOTO,K.TANAKA,K.KATO JRNL TITL MOLECULAR AND STRUCTURAL BASIS OF THE PROTEASOME ALPHA JRNL TITL 2 SUBUNIT ASSEMBLY MECHANISM MEDIATED BY THE JRNL TITL 3 PROTEASOME-ASSEMBLING CHAPERONE PAC3-PAC4 HETERODIMER. JRNL REF INT J MOL SCI V. 20 2019 JRNL REFN ESSN 1422-0067 JRNL PMID 31067643 JRNL DOI 10.3390/IJMS20092231 REMARK 2 REMARK 2 RESOLUTION. 0.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 0.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 83857 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.136 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.146 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.380 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 14.6569 - 2.3114 1.00 6075 146 0.1507 0.1566 REMARK 3 2 2.3114 - 1.8357 1.00 5929 144 0.1324 0.1439 REMARK 3 3 1.8357 - 1.6040 1.00 5902 145 0.1217 0.1332 REMARK 3 4 1.6040 - 1.4575 1.00 5851 143 0.1131 0.1198 REMARK 3 5 1.4575 - 1.3531 1.00 5848 142 0.1131 0.1287 REMARK 3 6 1.3531 - 1.2734 1.00 5808 144 0.1103 0.1246 REMARK 3 7 1.2734 - 1.2096 1.00 5855 143 0.1120 0.1205 REMARK 3 8 1.2096 - 1.1570 1.00 5826 142 0.1100 0.1171 REMARK 3 9 1.1570 - 1.1125 1.00 5831 142 0.1151 0.1288 REMARK 3 10 1.1125 - 1.0741 1.00 5806 142 0.1297 0.1291 REMARK 3 11 1.0741 - 1.0405 1.00 5793 143 0.1567 0.1778 REMARK 3 12 1.0405 - 1.0108 1.00 5847 146 0.1994 0.2357 REMARK 3 13 1.0108 - 0.9842 1.00 5781 139 0.2184 0.2459 REMARK 3 14 0.9842 - 0.9602 0.98 5706 138 0.2729 0.2645 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.190 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.008 939 REMARK 3 ANGLE : 1.051 1282 REMARK 3 CHIRALITY : 0.088 167 REMARK 3 PLANARITY : 0.008 159 REMARK 3 DIHEDRAL : 18.971 348 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 6JPT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-APR-19. REMARK 100 THE DEPOSITION ID IS D_1300011553. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-OCT-18 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90000 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83927 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.960 REMARK 200 RESOLUTION RANGE LOW (A) : 47.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.98 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 1.16200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2Z5E REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG2000 MONOMETHYL ETHER, 0.1 M REMARK 280 POTASSIUM THIOCYANATE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 15.69133 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 31.38267 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 31.38267 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 15.69133 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: 3230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -15.69133 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 322 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 443 LIES ON A SPECIAL POSITION. 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 HZ2 LYS A 65 O HOH A 304 1.58 REMARK 500 O HOH A 317 O HOH A 419 1.79 REMARK 500 O HOH A 397 O HOH A 424 2.04 REMARK 500 O HOH A 312 O HOH A 422 2.04 REMARK 500 O HOH A 425 O HOH A 427 2.13 REMARK 500 OD1 ASP A 103 O HOH A 301 2.19 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 ALA A 54 -127.75 -102.36 REMARK 500 REMARK 500 REMARK: NULL 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 465 DISTANCE = 5.94 ANGSTROMS REMARK 525 HOH A 466 DISTANCE = 6.02 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 202 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 393 O REMARK 620 2 HOH A 439 O 134.4 REMARK 620 3 HOH A 456 O 123.7 99.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SCN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Z5E RELATED DB: PDB DBREF 6JPT A 1 122 UNP Q9BT73 PSMG3_HUMAN 1 122 SEQRES 1 A 122 MET GLU ASP THR PRO LEU VAL ILE SER LYS GLN LYS THR SEQRES 2 A 122 GLU VAL VAL CYS GLY VAL PRO THR GLN VAL VAL CYS THR SEQRES 3 A 122 ALA PHE SER SER HIS ILE LEU VAL VAL VAL THR GLN PHE SEQRES 4 A 122 GLY LYS MET GLY THR LEU VAL SER LEU GLU PRO SER SER SEQRES 5 A 122 VAL ALA SER ASP VAL SER LYS PRO VAL LEU THR THR LYS SEQRES 6 A 122 VAL LEU LEU GLY GLN ASP GLU PRO LEU ILE HIS VAL PHE SEQRES 7 A 122 ALA LYS ASN LEU VAL ALA PHE VAL SER GLN GLU ALA GLY SEQRES 8 A 122 ASN ARG ALA VAL LEU LEU ALA VAL ALA VAL LYS ASP LYS SEQRES 9 A 122 SER MET GLU GLY LEU LYS ALA LEU ARG GLU VAL ILE ARG SEQRES 10 A 122 VAL CYS GLN VAL TRP HET SCN A 201 3 HET K A 202 1 HETNAM SCN THIOCYANATE ION HETNAM K POTASSIUM ION FORMUL 2 SCN C N S 1- FORMUL 3 K K 1+ FORMUL 4 HOH *166(H2 O) HELIX 1 AA1 GLU A 72 ALA A 90 1 19 HELIX 2 AA2 SER A 105 CYS A 119 1 15 SHEET 1 AA1 6 ILE A 8 VAL A 16 0 SHEET 2 AA1 6 VAL A 19 ALA A 27 -1 O VAL A 23 N LYS A 12 SHEET 3 AA1 6 HIS A 31 THR A 37 -1 O THR A 37 N GLN A 22 SHEET 4 AA1 6 ALA A 94 ALA A 100 1 O LEU A 96 N VAL A 34 SHEET 5 AA1 6 THR A 44 SER A 51 -1 N VAL A 46 O LEU A 97 SHEET 6 AA1 6 VAL A 61 LEU A 68 -1 O LEU A 67 N LEU A 45 LINK K K A 202 O HOH A 393 1555 1555 2.87 LINK K K A 202 O HOH A 439 1555 1555 2.60 LINK K K A 202 O HOH A 456 1555 1555 2.78 SITE 1 AC1 6 PRO A 20 PHE A 39 LEU A 74 ASN A 81 SITE 2 AC1 6 LEU A 109 HOH A 392 SITE 1 AC2 5 ALA A 100 LYS A 102 HOH A 393 HOH A 439 SITE 2 AC2 5 HOH A 456 CRYST1 71.229 71.229 47.074 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 0.014039 0.008106 0.000000 0.00000 SCALE2 0.000000 0.016211 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021243 0.00000