HEADER CHAPERONE 26-AUG-13 3WHJ TITLE CRYSTAL STRUCTURE OF NAS2 N-TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE 26S PROTEASOME REGULATORY SUBUNIT P27; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN, UNP RESIDUES 1-120; 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: 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-CODONPLUS(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PCOLD-MBP KEYWDS PROTEASOME ASSEMBLY CHAPERONE, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR T.SATOH,Y.SAEKI,T.HIROMOTO,Y.-H.WANG,Y.UEKUSA,H.YAGI,H.YOSHIHARA, AUTHOR 2 M.YAGI-UTSUMI,T.MIZUSHIMA,K.TANAKA,K.KATO REVDAT 3 24-AUG-22 3WHJ 1 JRNL REMARK SEQADV LINK REVDAT 2 16-APR-14 3WHJ 1 JRNL REVDAT 1 26-MAR-14 3WHJ 0 JRNL AUTH T.SATOH,Y.SAEKI,T.HIROMOTO,Y.H.WANG,Y.UEKUSA,H.YAGI, JRNL AUTH 2 H.YOSHIHARA,M.YAGI-UTSUMI,T.MIZUSHIMA,K.TANAKA,K.KATO JRNL TITL STRUCTURAL BASIS FOR PROTEASOME FORMATION CONTROLLED BY AN JRNL TITL 2 ASSEMBLY CHAPERONE NAS2. JRNL REF STRUCTURE V. 22 731 2014 JRNL REFN ISSN 0969-2126 JRNL PMID 24685148 JRNL DOI 10.1016/J.STR.2014.02.014 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0029 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 21760 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1176 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1551 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.1570 REMARK 3 BIN FREE R VALUE SET COUNT : 90 REMARK 3 BIN FREE R VALUE : 0.2190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 892 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 97 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.47000 REMARK 3 B22 (A**2) : -1.47000 REMARK 3 B33 (A**2) : 4.77000 REMARK 3 B12 (A**2) : -1.47000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.075 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.071 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.051 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.350 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.958 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 908 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 890 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1222 ; 1.571 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2048 ; 0.958 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 109 ; 5.828 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 45 ;39.536 ;26.444 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 183 ;14.655 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;23.898 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 146 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1006 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 192 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 1794 ; 3.442 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 41 ;46.124 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1853 ;21.497 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3WHJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000096342. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-AUG-12 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL13B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23180 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 45.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.20 REMARK 200 R MERGE FOR SHELL (I) : 0.39100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.9M SODIUM ACETATE TRIHYDRATE, 0.1M REMARK 280 HEPES (PH 8.5), 50MM CADMIUM SULFATE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 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 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 49.92000 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 99.84000 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 74.88000 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 124.80000 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 24.96000 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.92000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 99.84000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 124.80000 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 74.88000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 24.96000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 0.500000 0.866025 0.000000 -64.59000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 111.87316 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 24.96000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 0.500000 0.866025 0.000000 -32.29500 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 55.93658 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 24.96000 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 391 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 LEU A 63 REMARK 465 VAL A 64 REMARK 465 THR A 65 REMARK 465 PRO A 66 REMARK 465 ASP A 67 REMARK 465 GLY A 68 REMARK 465 ASP A 118 REMARK 465 ALA A 119 REMARK 465 ARG A 120 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 75 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ASP A 75 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 116 GLN A 117 148.29 REMARK 500 REMARK 500 REMARK: NULL 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 CD A 204 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 27 OD1 REMARK 620 2 ASP A 27 OD2 52.3 REMARK 620 3 HIS A 95 NE2 104.9 85.7 REMARK 620 4 SO4 A 201 O1 83.2 134.5 118.2 REMARK 620 5 SO4 A 201 O2 141.5 166.1 87.5 59.3 REMARK 620 6 SO4 A 201 S 111.6 163.9 99.7 30.2 29.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 205 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 38 NZ REMARK 620 2 GLU A 42 OE1 85.8 REMARK 620 3 GLU A 42 OE2 103.8 54.5 REMARK 620 4 SO4 A 202 O3 86.0 127.8 170.2 REMARK 620 5 SO4 A 202 S 76.1 99.8 153.8 28.6 REMARK 620 6 HOH A 330 O 161.4 89.3 87.7 82.9 87.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 203 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 92 OD2 REMARK 620 2 ASP A 92 OD1 53.7 REMARK 620 3 HOH A 305 O 84.6 81.9 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 SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 207 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WHK RELATED DB: PDB REMARK 900 RELATED ID: 3WHL RELATED DB: PDB REMARK 900 RELATED ID: 3VLD RELATED DB: PDB REMARK 900 RELATED ID: 3VLE RELATED DB: PDB REMARK 900 RELATED ID: 3VLF RELATED DB: PDB REMARK 900 RELATED ID: 3ACP RELATED DB: PDB REMARK 900 RELATED ID: 2DZN RELATED DB: PDB REMARK 900 RELATED ID: 3H4M RELATED DB: PDB DBREF 3WHJ A 1 120 UNP P40555 PSMD9_YEAST 1 120 SEQADV 3WHJ GLY A -1 UNP P40555 EXPRESSION TAG SEQADV 3WHJ SER A 0 UNP P40555 EXPRESSION TAG SEQRES 1 A 122 GLY SER MET GLU GLU GLU GLU LEU SER LYS LEU LEU ALA SEQRES 2 A 122 ASN VAL LYS ILE ASP PRO SER LEU THR SER ARG ILE SER SEQRES 3 A 122 GLN ILE ASP SER PHE LYS LEU SER GLU LEU MET VAL LEU SEQRES 4 A 122 LYS THR ASP ILE GLU THR GLN LEU GLU ALA TYR PHE SER SEQRES 5 A 122 VAL LEU GLU GLN GLN GLY ILE GLY MET ASP SER ALA LEU SEQRES 6 A 122 VAL THR PRO ASP GLY TYR PRO ARG SER ASP VAL ASP VAL SEQRES 7 A 122 LEU GLN VAL THR MET ILE ARG LYS ASN VAL ASN MET LEU SEQRES 8 A 122 LYS ASN ASP LEU ASN HIS LEU LEU GLN ARG SER HIS VAL SEQRES 9 A 122 LEU LEU ASN GLN HIS PHE ASP ASN MET ASN VAL LYS SER SEQRES 10 A 122 ASN GLN ASP ALA ARG HET SO4 A 201 5 HET SO4 A 202 5 HET CD A 203 1 HET CD A 204 1 HET CD A 205 1 HET CD A 206 1 HET CD A 207 1 HETNAM SO4 SULFATE ION HETNAM CD CADMIUM ION FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 CD 5(CD 2+) FORMUL 9 HOH *97(H2 O) HELIX 1 1 MET A 1 ASN A 12 1 12 HELIX 2 2 ASP A 16 GLN A 25 1 10 HELIX 3 3 LYS A 30 GLN A 55 1 26 HELIX 4 4 SER A 72 MET A 111 1 40 LINK OE2 GLU A 5 CD CD A 206 1555 1555 2.02 LINK OD1 ASP A 27 CD CD A 204 1555 1555 2.16 LINK OD2 ASP A 27 CD CD A 204 1555 1555 2.69 LINK NZ LYS A 38 CD CD A 205 1555 1555 2.30 LINK OE1 GLU A 42 CD CD A 205 1555 1555 2.35 LINK OE2 GLU A 42 CD CD A 205 1555 1555 2.44 LINK OD2 ASP A 92 CD CD A 203 1555 1555 2.38 LINK OD1 ASP A 92 CD CD A 203 1555 1555 2.50 LINK NE2 HIS A 95 CD CD A 204 1555 1555 2.28 LINK OD2 ASP A 109 CD CD A 207 1555 1555 2.11 LINK O1 SO4 A 201 CD CD A 204 1555 1555 2.30 LINK O2 SO4 A 201 CD CD A 204 1555 1555 2.68 LINK S SO4 A 201 CD CD A 204 1555 1555 2.81 LINK O3 SO4 A 202 CD CD A 205 1555 1555 2.43 LINK S SO4 A 202 CD CD A 205 1555 1555 3.05 LINK CD CD A 203 O HOH A 305 1555 1555 2.25 LINK CD CD A 205 O HOH A 330 1555 1555 2.34 SITE 1 AC1 9 ASP A 27 GLN A 54 TYR A 69 ASP A 75 SITE 2 AC1 9 HIS A 95 GLN A 98 ARG A 99 CD A 204 SITE 3 AC1 9 HOH A 320 SITE 1 AC2 9 LYS A 30 LYS A 38 THR A 39 GLU A 42 SITE 2 AC2 9 HIS A 107 CD A 205 HOH A 312 HOH A 318 SITE 3 AC2 9 HOH A 335 SITE 1 AC3 5 ASP A 73 ASP A 92 HOH A 302 HOH A 305 SITE 2 AC3 5 HOH A 341 SITE 1 AC4 4 ASP A 27 ASP A 75 HIS A 95 SO4 A 201 SITE 1 AC5 5 LYS A 38 GLU A 42 HIS A 107 SO4 A 202 SITE 2 AC5 5 HOH A 330 SITE 1 AC6 3 GLU A 5 ASP A 16 HOH A 382 SITE 1 AC7 1 ASP A 109 CRYST1 64.590 64.590 149.760 90.00 90.00 120.00 P 61 2 2 12 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 0.015483 0.008939 0.000000 0.00000 SCALE2 0.000000 0.017878 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006677 0.00000