HEADER HYDROLASE/SIGNALING PROTEIN 01-MAY-08 2ZNV TITLE CRYSTAL STRUCTURE OF HUMAN AMSH-LP DUB DOMAIN IN COMPLEX WITH LYS63- TITLE 2 LINKED UBIQUITIN DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMSH-LIKE PROTEASE; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: MPN DOMAIN, DUB DOMAIN, UNP RESIDUES 264-436; COMPND 5 SYNONYM: AMSH-LP, STAM-BINDING PROTEIN-LIKE 1; COMPND 6 EC: 3.1.2.15; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: UBIQUITIN; COMPND 11 CHAIN: B, E; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: UBIQUITIN; COMPND 16 CHAIN: C, F; COMPND 17 ENGINEERED: YES; COMPND 18 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PCOLD GST; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 12 ORGANISM_COMMON: MOUSE; SOURCE 13 ORGANISM_TAXID: 10090; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET26B; SOURCE 19 MOL_ID: 3; SOURCE 20 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 21 ORGANISM_COMMON: MOUSE; SOURCE 22 ORGANISM_TAXID: 10090; SOURCE 23 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 24 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 25 EXPRESSION_SYSTEM_STRAIN: ROSETTA (DE3); SOURCE 26 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 27 EXPRESSION_SYSTEM_PLASMID: PET26B KEYWDS PROTEIN COMPLEX, METAL BINDING PROTEIN, ALTERNATIVE SPLICING, KEYWDS 2 HYDROLASE, METAL-BINDING, METALLOPROTEASE, PROTEASE, UBL CONJUGATION KEYWDS 3 PATHWAY, ZINC, CYTOPLASM, NUCLEUS, PHOSPHOPROTEIN, HYDROLASE- KEYWDS 4 SIGNALING PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.SATO,Y.AZUSA,A.YAMAGATA,H.MIMURA,X.WANG,M.YAMASHITA,K.OOKATA, AUTHOR 2 O.NUREKI,K.IWAI,M.KOMADA,S.FUKAI REVDAT 5 01-NOV-23 2ZNV 1 REMARK REVDAT 4 10-NOV-21 2ZNV 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2ZNV 1 VERSN REVDAT 2 23-SEP-08 2ZNV 1 JRNL REVDAT 1 02-SEP-08 2ZNV 0 JRNL AUTH Y.SATO,A.YOSHIKAWA,A.YAMAGATA,H.MIMURA,M.YAMASHITA,K.OOKATA, JRNL AUTH 2 O.NUREKI,K.IWAI,M.KOMADA,S.FUKAI JRNL TITL STRUCTURAL BASIS FOR SPECIFIC CLEAVAGE OF LYS 63-LINKED JRNL TITL 2 POLYUBIQUITIN CHAINS JRNL REF NATURE V. 455 358 2008 JRNL REFN ISSN 0028-0836 JRNL PMID 18758443 JRNL DOI 10.1038/NATURE07254 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 77359 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4051 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5197 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2040 REMARK 3 BIN FREE R VALUE SET COUNT : 285 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5051 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 605 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.25000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : 0.27000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.15000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.097 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.096 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.059 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.629 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.932 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5177 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6987 ; 1.265 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 643 ; 5.747 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 222 ;33.822 ;24.955 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 982 ;12.863 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;17.307 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 828 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3756 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2246 ; 0.200 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3523 ; 0.306 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 447 ; 0.178 ; 0.200 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): 66 ; 0.218 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 51 ; 0.140 ; 0.200 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): 3291 ; 0.858 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5228 ; 1.480 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2040 ; 2.248 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1755 ; 3.724 ; 4.500 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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; THE DEPOSITORS HAVE NOTICED THAT 1.7 A IS OUT OF REMARK 3 RANGE FOR THE LINK BETWEEN THE GLY76 C ATOM AND THE LYS63 NZ REMARK 3 ATOM. HOWEVER, REFMAC5 REFINED THE BOND LENGTH UP TO 1.7 A, REMARK 3 DESPITE OF THE DECLARATION OF THE LINK RECORD. AND, ACTUALLY, REMARK 3 THE ELECTRON DENSITY MAP SHOWS A LITTLE BIT LONGER BONDING. SO, REMARK 3 THEY CONCLUDED THAT THIS ATYPICAL BONDING LIKELY OCCURS IN THEIR REMARK 3 STRUCTURE. REMARK 4 REMARK 4 2ZNV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000028203. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83683 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 87.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -0.500 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.26700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 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: PDB ENTRIES 2ZNR AND 1UBQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 180MM TRI-AMMONIUM CITRATE (PH 7.0), REMARK 280 24% PEG 3350, 3% 1,6-HEXANEDIOL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 48.68150 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5, 6 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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: 5 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E 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: 6 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: F 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 259 REMARK 465 PRO A 260 REMARK 465 GLY A 261 REMARK 465 HIS A 262 REMARK 465 MET A 263 REMARK 465 GLU A 264 REMARK 465 GLY D 259 REMARK 465 PRO D 260 REMARK 465 GLY D 261 REMARK 465 HIS D 262 REMARK 465 MET D 263 REMARK 465 GLU D 264 REMARK 465 LEU F 8 REMARK 465 THR F 9 REMARK 465 GLY F 10 REMARK 465 LEU F 71 REMARK 465 ARG F 72 REMARK 465 LEU F 73 REMARK 465 ARG F 74 REMARK 465 GLY F 75 REMARK 465 GLY F 76 REMARK 465 ASP F 77 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 SG CYS A 298 O HOH A 509 1.85 REMARK 500 O HOH A 562 O HOH A 586 1.92 REMARK 500 NH2 ARG A 390 O HOH A 585 1.94 REMARK 500 CB CYS A 298 O HOH A 509 1.99 REMARK 500 O HOH D 543 O HOH D 596 2.05 REMARK 500 O HOH D 441 O HOH D 566 2.07 REMARK 500 O HOH C 79 O HOH C 146 2.08 REMARK 500 O HOH D 464 O HOH D 575 2.11 REMARK 500 O HOH D 577 O HOH D 587 2.15 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 GLU A 326 -138.76 -86.75 REMARK 500 SER A 380 78.70 -118.33 REMARK 500 HIS D 303 -91.41 59.96 REMARK 500 ASN D 327 144.66 177.35 REMARK 500 SER D 380 78.80 -118.07 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 ZN A 1 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 362 NE2 REMARK 620 2 CYS A 402 SG 112.3 REMARK 620 3 HIS A 408 NE2 106.3 108.9 REMARK 620 4 HIS A 410 NE2 111.8 115.1 101.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 362 NE2 REMARK 620 2 CYS D 402 SG 113.2 REMARK 620 3 HIS D 408 NE2 109.7 110.7 REMARK 620 4 HIS D 410 NE2 117.4 94.2 110.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 77 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO D 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZNR RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX WITH PR(III) DBREF 2ZNV A 264 436 UNP Q96FJ0 STALP_HUMAN 264 436 DBREF 2ZNV B 1 76 UNP P62991 UBIQ_MOUSE 1 76 DBREF 2ZNV C 1 76 UNP P62991 UBIQ_MOUSE 1 76 DBREF 2ZNV D 264 436 UNP Q96FJ0 STALP_HUMAN 264 436 DBREF 2ZNV E 1 76 UNP P62991 UBIQ_MOUSE 1 76 DBREF 2ZNV F 1 76 UNP P62991 UBIQ_MOUSE 1 76 SEQADV 2ZNV GLY A 259 UNP Q96FJ0 EXPRESSION TAG SEQADV 2ZNV PRO A 260 UNP Q96FJ0 EXPRESSION TAG SEQADV 2ZNV GLY A 261 UNP Q96FJ0 EXPRESSION TAG SEQADV 2ZNV HIS A 262 UNP Q96FJ0 EXPRESSION TAG SEQADV 2ZNV MET A 263 UNP Q96FJ0 EXPRESSION TAG SEQADV 2ZNV ALA A 292 UNP Q96FJ0 GLU 292 ENGINEERED MUTATION SEQADV 2ZNV ARG B 63 UNP P62991 LYS 63 ENGINEERED MUTATION SEQADV 2ZNV ASP C 77 UNP P62991 ENGINEERED MUTATION SEQADV 2ZNV GLY D 259 UNP Q96FJ0 EXPRESSION TAG SEQADV 2ZNV PRO D 260 UNP Q96FJ0 EXPRESSION TAG SEQADV 2ZNV GLY D 261 UNP Q96FJ0 EXPRESSION TAG SEQADV 2ZNV HIS D 262 UNP Q96FJ0 EXPRESSION TAG SEQADV 2ZNV MET D 263 UNP Q96FJ0 EXPRESSION TAG SEQADV 2ZNV ALA D 292 UNP Q96FJ0 GLU 292 ENGINEERED MUTATION SEQADV 2ZNV ARG E 63 UNP P62991 LYS 63 ENGINEERED MUTATION SEQADV 2ZNV ASP F 77 UNP P62991 ENGINEERED MUTATION SEQRES 1 A 178 GLY PRO GLY HIS MET GLU GLY LEU ARG CYS VAL VAL LEU SEQRES 2 A 178 PRO GLU ASP LEU CYS HIS LYS PHE LEU GLN LEU ALA GLU SEQRES 3 A 178 SER ASN THR VAL ARG GLY ILE ALA THR CYS GLY ILE LEU SEQRES 4 A 178 CYS GLY LYS LEU THR HIS ASN GLU PHE THR ILE THR HIS SEQRES 5 A 178 VAL ILE VAL PRO LYS GLN SER ALA GLY PRO ASP TYR CYS SEQRES 6 A 178 ASP MET GLU ASN VAL GLU GLU LEU PHE ASN VAL GLN ASP SEQRES 7 A 178 GLN HIS ASP LEU LEU THR LEU GLY TRP ILE HIS THR HIS SEQRES 8 A 178 PRO THR GLN THR ALA PHE LEU SER SER VAL ASP LEU HIS SEQRES 9 A 178 THR HIS CYS SER TYR GLN LEU MET LEU PRO GLU ALA ILE SEQRES 10 A 178 ALA ILE VAL CYS SER PRO LYS HIS LYS ASP THR GLY ILE SEQRES 11 A 178 PHE ARG LEU THR ASN ALA GLY MET LEU GLU VAL SER ALA SEQRES 12 A 178 CYS LYS LYS LYS GLY PHE HIS PRO HIS THR LYS GLU PRO SEQRES 13 A 178 ARG LEU PHE SER ILE CYS LYS HIS VAL LEU VAL LYS ASP SEQRES 14 A 178 ILE LYS ILE ILE VAL LEU ASP LEU ARG SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN ARG GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 C 77 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 77 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 77 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 C 77 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 C 77 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 C 77 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY ASP SEQRES 1 D 178 GLY PRO GLY HIS MET GLU GLY LEU ARG CYS VAL VAL LEU SEQRES 2 D 178 PRO GLU ASP LEU CYS HIS LYS PHE LEU GLN LEU ALA GLU SEQRES 3 D 178 SER ASN THR VAL ARG GLY ILE ALA THR CYS GLY ILE LEU SEQRES 4 D 178 CYS GLY LYS LEU THR HIS ASN GLU PHE THR ILE THR HIS SEQRES 5 D 178 VAL ILE VAL PRO LYS GLN SER ALA GLY PRO ASP TYR CYS SEQRES 6 D 178 ASP MET GLU ASN VAL GLU GLU LEU PHE ASN VAL GLN ASP SEQRES 7 D 178 GLN HIS ASP LEU LEU THR LEU GLY TRP ILE HIS THR HIS SEQRES 8 D 178 PRO THR GLN THR ALA PHE LEU SER SER VAL ASP LEU HIS SEQRES 9 D 178 THR HIS CYS SER TYR GLN LEU MET LEU PRO GLU ALA ILE SEQRES 10 D 178 ALA ILE VAL CYS SER PRO LYS HIS LYS ASP THR GLY ILE SEQRES 11 D 178 PHE ARG LEU THR ASN ALA GLY MET LEU GLU VAL SER ALA SEQRES 12 D 178 CYS LYS LYS LYS GLY PHE HIS PRO HIS THR LYS GLU PRO SEQRES 13 D 178 ARG LEU PHE SER ILE CYS LYS HIS VAL LEU VAL LYS ASP SEQRES 14 D 178 ILE LYS ILE ILE VAL LEU ASP LEU ARG SEQRES 1 E 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 E 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 E 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 E 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 E 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN ARG GLU SER SEQRES 6 E 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 F 77 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 F 77 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 F 77 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 F 77 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 F 77 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 F 77 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY ASP HET ZN A 1 1 HET EDO A 2 4 HET EDO B 77 4 HET ZN D 2 1 HET EDO D 3 4 HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 7 ZN 2(ZN 2+) FORMUL 8 EDO 3(C2 H6 O2) FORMUL 12 HOH *605(H2 O) HELIX 1 1 ASP A 274 VAL A 288 1 15 HELIX 2 2 VAL A 328 HIS A 338 1 11 HELIX 3 3 SER A 357 LEU A 371 1 15 HELIX 4 4 PRO A 381 LYS A 384 5 4 HELIX 5 5 THR A 392 CYS A 402 1 11 HELIX 6 6 THR B 22 GLY B 35 1 14 HELIX 7 7 PRO B 37 ASP B 39 5 3 HELIX 8 8 LEU B 56 ASN B 60 5 5 HELIX 9 9 THR C 22 GLY C 35 1 14 HELIX 10 10 PRO C 37 GLN C 41 5 5 HELIX 11 11 THR C 55 ASN C 60 5 6 HELIX 12 12 ASP D 274 VAL D 288 1 15 HELIX 13 13 VAL D 328 ASP D 339 1 12 HELIX 14 14 SER D 357 LEU D 371 1 15 HELIX 15 15 PRO D 381 LYS D 384 5 4 HELIX 16 16 THR D 392 ALA D 401 1 10 HELIX 17 17 THR E 22 GLY E 35 1 14 HELIX 18 18 PRO E 37 ASP E 39 5 3 HELIX 19 19 THR F 22 GLY F 35 1 14 HELIX 20 20 PRO F 37 GLN F 41 5 5 HELIX 21 21 LEU F 56 ASN F 60 5 5 SHEET 1 A 8 PHE A 417 ILE A 419 0 SHEET 2 A 8 ASP A 385 LEU A 391 -1 N ARG A 390 O SER A 418 SHEET 3 A 8 ILE A 375 SER A 380 -1 N ALA A 376 O PHE A 389 SHEET 4 A 8 LEU A 341 THR A 348 1 N TRP A 345 O ILE A 377 SHEET 5 A 8 CYS A 294 THR A 302 -1 N LEU A 297 O LEU A 343 SHEET 6 A 8 GLU A 305 VAL A 313 -1 O ILE A 312 N ILE A 296 SHEET 7 A 8 VAL A 269 PRO A 272 1 N VAL A 270 O PHE A 306 SHEET 8 A 8 VAL A 423 LYS A 426 1 O LEU A 424 N VAL A 269 SHEET 1 B 7 PHE A 417 ILE A 419 0 SHEET 2 B 7 ASP A 385 LEU A 391 -1 N ARG A 390 O SER A 418 SHEET 3 B 7 ILE A 375 SER A 380 -1 N ALA A 376 O PHE A 389 SHEET 4 B 7 LEU A 341 THR A 348 1 N TRP A 345 O ILE A 377 SHEET 5 B 7 CYS A 294 THR A 302 -1 N LEU A 297 O LEU A 343 SHEET 6 B 7 GLU A 305 VAL A 313 -1 O ILE A 312 N ILE A 296 SHEET 7 B 7 ILE A 431 ASP A 434 1 O LEU A 433 N VAL A 313 SHEET 1 C 3 GLN A 316 ALA A 318 0 SHEET 2 C 3 CYS A 323 MET A 325 -1 O ASP A 324 N SER A 317 SHEET 3 C 3 ARG B 74 GLY B 75 -1 O GLY B 75 N CYS A 323 SHEET 1 D 5 THR B 12 GLU B 16 0 SHEET 2 D 5 GLN B 2 LYS B 6 -1 N VAL B 5 O ILE B 13 SHEET 3 D 5 THR B 66 LEU B 71 1 O LEU B 67 N PHE B 4 SHEET 4 D 5 GLN B 41 PHE B 45 -1 N ARG B 42 O VAL B 70 SHEET 5 D 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SHEET 1 E 5 THR C 12 GLU C 16 0 SHEET 2 E 5 GLN C 2 LYS C 6 -1 N ILE C 3 O LEU C 15 SHEET 3 E 5 THR C 66 LEU C 69 1 O LEU C 67 N LYS C 6 SHEET 4 E 5 LEU C 43 PHE C 45 -1 N ILE C 44 O HIS C 68 SHEET 5 E 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 SHEET 1 F 8 PHE D 417 ILE D 419 0 SHEET 2 F 8 ASP D 385 LEU D 391 -1 N ARG D 390 O SER D 418 SHEET 3 F 8 ILE D 375 SER D 380 -1 N SER D 380 O ASP D 385 SHEET 4 F 8 LEU D 341 THR D 348 1 N TRP D 345 O ILE D 377 SHEET 5 F 8 CYS D 294 THR D 302 -1 N GLY D 299 O LEU D 341 SHEET 6 F 8 GLU D 305 VAL D 313 -1 O ILE D 312 N ILE D 296 SHEET 7 F 8 VAL D 269 PRO D 272 1 N VAL D 270 O ILE D 308 SHEET 8 F 8 VAL D 423 LYS D 426 1 O LEU D 424 N LEU D 271 SHEET 1 G 7 PHE D 417 ILE D 419 0 SHEET 2 G 7 ASP D 385 LEU D 391 -1 N ARG D 390 O SER D 418 SHEET 3 G 7 ILE D 375 SER D 380 -1 N SER D 380 O ASP D 385 SHEET 4 G 7 LEU D 341 THR D 348 1 N TRP D 345 O ILE D 377 SHEET 5 G 7 CYS D 294 THR D 302 -1 N GLY D 299 O LEU D 341 SHEET 6 G 7 GLU D 305 VAL D 313 -1 O ILE D 312 N ILE D 296 SHEET 7 G 7 ILE D 431 ASP D 434 1 O LEU D 433 N VAL D 313 SHEET 1 H 3 GLN D 316 ALA D 318 0 SHEET 2 H 3 CYS D 323 MET D 325 -1 O ASP D 324 N SER D 317 SHEET 3 H 3 ARG E 74 GLY E 75 -1 O GLY E 75 N CYS D 323 SHEET 1 I 5 THR E 12 GLU E 16 0 SHEET 2 I 5 GLN E 2 LYS E 6 -1 N VAL E 5 O ILE E 13 SHEET 3 I 5 THR E 66 LEU E 71 1 O LEU E 67 N PHE E 4 SHEET 4 I 5 GLN E 41 PHE E 45 -1 N ARG E 42 O VAL E 70 SHEET 5 I 5 LYS E 48 GLN E 49 -1 O LYS E 48 N PHE E 45 SHEET 1 J 5 ILE F 13 GLU F 16 0 SHEET 2 J 5 GLN F 2 LYS F 6 -1 N ILE F 3 O LEU F 15 SHEET 3 J 5 THR F 66 VAL F 70 1 O LEU F 67 N PHE F 4 SHEET 4 J 5 ARG F 42 PHE F 45 -1 N ARG F 42 O VAL F 70 SHEET 5 J 5 LYS F 48 GLN F 49 -1 O LYS F 48 N PHE F 45 LINK C GLY B 76 NZ LYS C 63 1555 1555 1.74 LINK C GLY E 76 NZ LYS F 63 1555 1555 1.30 LINK ZN ZN A 1 NE2 HIS A 362 1555 1555 2.08 LINK ZN ZN A 1 SG CYS A 402 1555 1555 2.31 LINK ZN ZN A 1 NE2 HIS A 408 1555 1555 2.06 LINK ZN ZN A 1 NE2 HIS A 410 1555 1555 2.06 LINK ZN ZN D 2 NE2 HIS D 362 1555 1555 2.04 LINK ZN ZN D 2 SG CYS D 402 1555 1555 2.31 LINK ZN ZN D 2 NE2 HIS D 408 1555 1555 2.04 LINK ZN ZN D 2 NE2 HIS D 410 1555 1555 2.04 CISPEP 1 GLU A 413 PRO A 414 0 -5.73 CISPEP 2 GLU D 413 PRO D 414 0 4.39 SITE 1 AC1 4 HIS A 362 CYS A 402 HIS A 408 HIS A 410 SITE 1 AC2 4 HIS D 362 CYS D 402 HIS D 408 HIS D 410 SITE 1 AC3 7 HIS A 362 SER A 366 SER A 400 HOH A 528 SITE 2 AC3 7 GLY B 35 PRO B 37 GLN B 40 SITE 1 AC4 6 HOH A 439 THR B 7 LEU B 8 LEU B 69 SITE 2 AC4 6 VAL B 70 LEU B 71 SITE 1 AC5 7 ASP C 32 VAL D 359 LYS D 405 GLY D 406 SITE 2 AC5 7 PHE D 407 HOH D 610 ARG E 74 CRYST1 38.089 97.363 87.894 90.00 97.49 90.00 P 1 21 1 4 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 0.026254 0.000000 0.003450 0.00000 SCALE2 0.000000 0.010271 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011475 0.00000