HEADER HYDROLASE 30-JUN-14 2MQW TITLE SOLUTION STRUCTURE OF A PROTEASOME RELATED SUBUNIT N TERMINAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 26S PROTEASOME REGULATORY SUBUNIT RPN9; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N TERMINAL DOMAIN, UNP RESIDUES 1-160; COMPND 5 SYNONYM: PROTEASOME NON-ATPASE SUBUNIT 7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 GENE: D9461.14, NAS7, RPN9, YDR427W; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28A KEYWDS A-HELIX BUNDLE, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.WU,Y.HU,C.JIN REVDAT 2 12-APR-17 2MQW 1 JRNL REVDAT 1 04-FEB-15 2MQW 0 JRNL AUTH Y.HU,Y.WU,Q.LI,W.ZHANG,C.JIN JRNL TITL SOLUTION STRUCTURE OF YEAST RPN9: INSIGHTS INTO PROTEASOME JRNL TITL 2 LID ASSEMBLY. JRNL REF J. BIOL. CHEM. V. 290 6878 2015 JRNL REFN ESSN 1083-351X JRNL PMID 25631053 JRNL DOI 10.1074/JBC.M114.626762 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MQW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUL-14. REMARK 100 THE DEPOSITION ID IS D_1000103944. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 210 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN-1, 50 MM SODIUM REMARK 210 PHOSPHATE-2, 100 MM SODIUM REMARK 210 CHLORIDE-3, 90% H2O/10% D2O; 0.5 REMARK 210 MM [U-100% 15N] PROTEIN-4, 50 MM REMARK 210 SODIUM PHOSPHATE-5, 100 MM REMARK 210 SODIUM CHLORIDE-6, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY ALIPHATIC; 3D HCCH- REMARK 210 COSY; 3D HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 OD1 ASP A 19 HG SER A 21 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 8 ARG A 115 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 10 ARG A 115 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 12 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 15 ARG A 115 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 18 ARG A 147 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES 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 1 LYS A 36 26.76 48.10 REMARK 500 1 SER A 54 43.44 -151.33 REMARK 500 1 PHE A 65 -58.27 -125.56 REMARK 500 1 PHE A 69 12.99 -147.12 REMARK 500 1 PHE A 92 -29.35 -153.54 REMARK 500 1 GLN A 114 148.23 123.60 REMARK 500 1 HIS A 122 18.34 -147.37 REMARK 500 1 VAL A 144 35.27 -74.08 REMARK 500 1 LYS A 145 -106.19 30.13 REMARK 500 1 ASP A 152 50.63 -150.73 REMARK 500 1 LEU A 153 17.40 -67.83 REMARK 500 1 ASP A 158 -47.18 -148.76 REMARK 500 2 SER A 54 47.69 -143.18 REMARK 500 2 PHE A 69 33.74 -141.12 REMARK 500 2 GLN A 114 19.51 -141.89 REMARK 500 2 ARG A 115 43.23 -151.06 REMARK 500 2 HIS A 122 -6.28 -141.20 REMARK 500 2 ASN A 141 -33.32 -141.15 REMARK 500 2 LEU A 143 -49.92 62.71 REMARK 500 2 ARG A 147 73.49 -151.14 REMARK 500 2 GLU A 154 -9.99 -58.82 REMARK 500 2 LEU A 157 -34.33 62.59 REMARK 500 3 ASN A 64 15.36 -143.57 REMARK 500 3 PHE A 65 -52.78 -125.68 REMARK 500 3 PHE A 69 25.71 -148.17 REMARK 500 3 ASP A 93 -51.00 -128.11 REMARK 500 3 GLN A 114 171.45 119.00 REMARK 500 3 ASN A 117 15.88 56.18 REMARK 500 3 HIS A 122 -32.62 69.00 REMARK 500 3 LEU A 143 46.29 -76.86 REMARK 500 4 LYS A 36 26.21 46.46 REMARK 500 4 SER A 54 37.63 -148.06 REMARK 500 4 PHE A 65 -70.33 -132.94 REMARK 500 4 PHE A 69 35.45 -148.06 REMARK 500 4 PHE A 92 -39.59 -143.68 REMARK 500 4 LYS A 140 53.67 32.67 REMARK 500 4 LEU A 143 88.30 -156.58 REMARK 500 4 LEU A 153 -62.99 -158.78 REMARK 500 5 ALA A 52 -105.78 48.29 REMARK 500 5 LYS A 53 -47.18 64.76 REMARK 500 5 SER A 54 43.54 -151.85 REMARK 500 5 ASN A 64 13.10 -143.45 REMARK 500 5 PHE A 65 -60.78 -122.00 REMARK 500 5 PHE A 69 20.79 -141.62 REMARK 500 5 ASP A 93 -50.98 -135.90 REMARK 500 5 GLN A 114 33.94 -81.68 REMARK 500 5 ASN A 116 83.21 -66.50 REMARK 500 5 SER A 119 15.57 -161.26 REMARK 500 5 LYS A 155 32.65 -86.47 REMARK 500 6 ALA A 52 18.24 54.88 REMARK 500 REMARK 500 THIS ENTRY HAS 168 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 58 0.11 SIDE CHAIN REMARK 500 2 TYR A 62 0.11 SIDE CHAIN REMARK 500 3 PHE A 29 0.08 SIDE CHAIN REMARK 500 3 TYR A 33 0.08 SIDE CHAIN REMARK 500 3 TYR A 62 0.07 SIDE CHAIN REMARK 500 5 PHE A 29 0.09 SIDE CHAIN REMARK 500 8 TYR A 62 0.07 SIDE CHAIN REMARK 500 9 ARG A 58 0.11 SIDE CHAIN REMARK 500 11 TYR A 62 0.07 SIDE CHAIN REMARK 500 13 TYR A 62 0.16 SIDE CHAIN REMARK 500 15 ARG A 58 0.12 SIDE CHAIN REMARK 500 16 TYR A 62 0.08 SIDE CHAIN REMARK 500 20 ARG A 58 0.11 SIDE CHAIN REMARK 500 20 TYR A 62 0.14 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19220 RELATED DB: BMRB REMARK 900 RELATED ID: 2MQX RELATED DB: PDB REMARK 900 RELATED ID: 2MR3 RELATED DB: PDB DBREF 2MQW A 1 160 UNP Q04062 RPN9_YEAST 1 160 SEQADV 2MQW GLY A -2 UNP Q04062 EXPRESSION TAG SEQADV 2MQW SER A -1 UNP Q04062 EXPRESSION TAG SEQADV 2MQW HIS A 0 UNP Q04062 EXPRESSION TAG SEQRES 1 A 163 GLY SER HIS MET PHE ASN ASN HIS GLU ILE ASP THR ILE SEQRES 2 A 163 LEU SER THR LEU ARG MET GLU ALA ASP PRO SER LEU HIS SEQRES 3 A 163 PRO LEU PHE GLU GLN PHE GLU LYS PHE TYR GLU GLU LYS SEQRES 4 A 163 LEU TRP PHE GLN LEU SER GLU SER LEU THR LYS PHE PHE SEQRES 5 A 163 ASP ASP ALA LYS SER THR PRO LEU ARG LEU ARG LEU TYR SEQRES 6 A 163 ASP ASN PHE VAL SER LYS PHE TYR ASP LYS ILE ASN GLN SEQRES 7 A 163 LEU SER VAL VAL LYS TYR LEU LEU ALA SER LEU LYS ASP SEQRES 8 A 163 SER LYS ASP PHE ASP GLU SER LEU LYS TYR LEU ASP ASP SEQRES 9 A 163 LEU LYS ALA GLN PHE GLN GLU LEU ASP SER LYS LYS GLN SEQRES 10 A 163 ARG ASN ASN GLY SER LYS ASP HIS GLY ASP GLY ILE LEU SEQRES 11 A 163 LEU ILE ASP SER GLU ILE ALA ARG THR TYR LEU LEU LYS SEQRES 12 A 163 ASN ASP LEU VAL LYS ALA ARG ASP LEU LEU ASP ASP LEU SEQRES 13 A 163 GLU LYS THR LEU ASP LYS LYS HELIX 1 1 ASN A 4 ALA A 18 1 15 HELIX 2 2 ASP A 19 SER A 21 5 3 HELIX 3 3 LEU A 22 GLU A 35 1 14 HELIX 4 4 LEU A 37 ASP A 50 1 14 HELIX 5 5 PRO A 56 PHE A 65 1 10 HELIX 6 6 VAL A 66 ILE A 73 5 8 HELIX 7 7 ASN A 74 SER A 89 1 16 HELIX 8 8 PHE A 92 GLN A 114 1 23 HELIX 9 9 GLY A 123 LYS A 140 1 18 HELIX 10 10 ALA A 146 LEU A 153 5 8 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1