HEADER CHAPERONE 13-DEC-13 4O06 TITLE 1.15A RESOLUTION STRUCTURE OF THE PROTEASOME ASSEMBLY CHAPERONE NAS2 TITLE 2 PDZ DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE 26S PROTEASOME REGULATORY SUBUNIT P27; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ DOMAIN (RESIDUES 126-220); COMPND 5 SYNONYM: PROTEASOME NON-ATPASE SUBUNIT 2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: NAS2, YIL007C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PGR608 KEYWDS NAS2, CHAPERONE, PROTEASOME, PDZ DOMAIN EXPDTA X-RAY DIFFRACTION AUTHOR S.LOVELL,N.MEHZABEEN,K.P.BATTAILE,C.R.SINGH,W.Q.CHOWDHURY,E.GEANES, AUTHOR 2 J.ROELOFS REVDAT 3 20-SEP-23 4O06 1 REMARK SEQADV REVDAT 2 22-NOV-17 4O06 1 REMARK REVDAT 1 16-APR-14 4O06 0 JRNL AUTH C.R.SINGH,S.LOVELL,N.MEHZABEEN,W.Q.CHOWDHURY,E.S.GEANES, JRNL AUTH 2 K.P.BATTAILE,J.ROELOFS JRNL TITL 1.15 ANGSTROM RESOLUTION STRUCTURE OF THE JRNL TITL 2 PROTEASOME-ASSEMBLY CHAPERONE NAS2 PDZ DOMAIN. JRNL REF ACTA CRYSTALLOGR F STRUCT V. 70 418 2014 JRNL REF 2 BIOL COMMUN JRNL REFN JRNL PMID 24699731 JRNL DOI 10.1107/S2053230X14003884 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1563 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.230 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 33494 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.194 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1698 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 32.9083 - 2.6324 1.00 2967 156 0.1964 0.2110 REMARK 3 2 2.6324 - 2.0895 1.00 2777 143 0.1737 0.1878 REMARK 3 3 2.0895 - 1.8254 0.99 2703 154 0.1555 0.1581 REMARK 3 4 1.8254 - 1.6585 0.99 2682 152 0.1492 0.1876 REMARK 3 5 1.6585 - 1.5397 0.98 2644 140 0.1414 0.1708 REMARK 3 6 1.5397 - 1.4489 0.98 2660 122 0.1385 0.2014 REMARK 3 7 1.4489 - 1.3763 0.97 2587 147 0.1394 0.1846 REMARK 3 8 1.3763 - 1.3164 0.97 2590 143 0.1420 0.1950 REMARK 3 9 1.3164 - 1.2657 0.96 2574 151 0.1510 0.2078 REMARK 3 10 1.2657 - 1.2221 0.96 2548 131 0.1591 0.1793 REMARK 3 11 1.2221 - 1.1838 0.95 2534 142 0.1723 0.2250 REMARK 3 12 1.1838 - 1.1500 0.95 2530 117 0.2183 0.2498 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.97 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 : 0.012 834 REMARK 3 ANGLE : 1.356 1137 REMARK 3 CHIRALITY : 0.103 132 REMARK 3 PLANARITY : 0.012 148 REMARK 3 DIHEDRAL : 14.754 331 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 4O06 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083875. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 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 : XSCALE REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.2.8, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33545 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 39.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 17.60 REMARK 200 R MERGE FOR SHELL (I) : 0.10700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: 3RLE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% (W/V) PEG 2000MME, 100 MM SODIUM REMARK 280 ACETATE, 200 MM AMMONIUM SULFATE, PH 5.5, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 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 57.91350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 19.98400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 19.98400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.95675 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 19.98400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 19.98400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 86.87025 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 19.98400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 19.98400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.95675 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 19.98400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 19.98400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 86.87025 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 57.91350 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 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 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 442 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 SER A 125 REMARK 465 GLN A 126 REMARK 465 ALA A 127 REMARK 465 ILE A 128 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 LEU A 117 CG CD1 CD2 REMARK 470 GLN A 172 CD OE1 NE2 REMARK 470 ARG A 210 NE CZ NH1 NH2 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 418 O HOH A 487 2.11 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 154 -4.07 81.39 REMARK 500 LEU A 171 -10.71 78.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PG4 A 301 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 302 DBREF 4O06 A 126 220 UNP P40555 PSMD9_YEAST 126 220 SEQADV 4O06 GLY A 115 UNP P40555 EXPRESSION TAG SEQADV 4O06 PRO A 116 UNP P40555 EXPRESSION TAG SEQADV 4O06 LEU A 117 UNP P40555 EXPRESSION TAG SEQADV 4O06 THR A 118 UNP P40555 EXPRESSION TAG SEQADV 4O06 ARG A 119 UNP P40555 EXPRESSION TAG SEQADV 4O06 ARG A 120 UNP P40555 EXPRESSION TAG SEQADV 4O06 ALA A 121 UNP P40555 EXPRESSION TAG SEQADV 4O06 SER A 122 UNP P40555 EXPRESSION TAG SEQADV 4O06 VAL A 123 UNP P40555 EXPRESSION TAG SEQADV 4O06 GLY A 124 UNP P40555 EXPRESSION TAG SEQADV 4O06 SER A 125 UNP P40555 EXPRESSION TAG SEQRES 1 A 106 GLY PRO LEU THR ARG ARG ALA SER VAL GLY SER GLN ALA SEQRES 2 A 106 ILE GLN TYR THR ILE PRO PHE ALA PHE ILE SER GLU VAL SEQRES 3 A 106 VAL PRO GLY SER PRO SER ASP LYS ALA ASP ILE LYS VAL SEQRES 4 A 106 ASP ASP LYS LEU ILE SER ILE GLY ASN VAL HIS ALA ALA SEQRES 5 A 106 ASN HIS SER LYS LEU GLN ASN ILE GLN MET VAL VAL MET SEQRES 6 A 106 LYS ASN GLU ASP ARG PRO LEU PRO VAL LEU LEU LEU ARG SEQRES 7 A 106 GLU GLY GLN ILE LEU LYS THR SER LEU THR PRO SER ARG SEQRES 8 A 106 ASN TRP ASN GLY ARG GLY LEU LEU GLY CYS ARG ILE GLN SEQRES 9 A 106 GLU LEU HET PG4 A 301 8 HET SO4 A 302 5 HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM SO4 SULFATE ION FORMUL 2 PG4 C8 H18 O5 FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *98(H2 O) HELIX 1 1 SER A 144 ALA A 149 1 6 HELIX 2 2 LEU A 171 ASN A 181 1 11 SHEET 1 A 5 GLN A 195 LEU A 201 0 SHEET 2 A 5 LEU A 186 ARG A 192 -1 N VAL A 188 O THR A 199 SHEET 3 A 5 LYS A 156 ILE A 160 -1 N ILE A 158 O LEU A 189 SHEET 4 A 5 ALA A 135 VAL A 140 -1 N ALA A 135 O LEU A 157 SHEET 5 A 5 CYS A 215 GLU A 219 -1 O GLN A 218 N PHE A 136 SITE 1 AC1 8 PRO A 185 LEU A 186 PRO A 187 LYS A 198 SITE 2 AC1 8 SER A 200 HOH A 413 HOH A 426 HOH A 498 SITE 1 AC2 4 ARG A 119 ARG A 120 GLN A 218 HOH A 466 CRYST1 39.968 39.968 115.827 90.00 90.00 90.00 P 41 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 0.025020 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025020 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008634 0.00000