10 20 30 40 50 60 70 80 1X23 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric Unit
HEADER LIGASE 19-APR-05 1X23
TITLE CRYSTAL STRUCTURE OF UBCH5C
COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D3; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: UBIQUITIN-PROTEIN LIGASE D3, UBIQUITIN CARRIER COMPND 5 PROTEIN D3, UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 3, E217, COMPND 6 KB 3; COMPND 7 EC: 6.3.2.19; COMPND 8 ENGINEERED: 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_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX6P-1
KEYWDS UBIQUITIN CONJUGATING ENZYME, UBIQUITIN, E2, LIGASE
EXPDTA X-RAY DIFFRACTION
AUTHOR M.NAKANISHI,N.TESHIMA,T.MIZUSHIMA,S.MURATA,K.TANAKA,T.YAMANE
REVDAT 2 24-FEB-09 1X23 1 VERSN REVDAT 1 03-MAY-05 1X23 0
JRNL AUTH M.NAKANISHI,N.TESHIMA,T.MIZUSHIMA,S.MURATA, JRNL AUTH 2 K.TANAKA,T.YAMANE JRNL TITL CRYSTAL STRUCTURE OF UBCH5C JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 41012 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2178 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2682 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.1960 REMARK 3 BIN FREE R VALUE SET COUNT : 151 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4867 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 677 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.61000 REMARK 3 B22 (A**2) : -0.55000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.57000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.207 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.199 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.132 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.156 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.951 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5012 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6829 ; 1.467 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 603 ; 6.089 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 220 ;37.404 ;23.636 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 808 ;17.039 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;17.452 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 733 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3872 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2627 ; 0.240 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3400 ; 0.321 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 549 ; 0.247 ; 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): 138 ; 0.225 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 89 ; 0.180 ; 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): 3157 ; 0.993 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5046 ; 1.611 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2115 ; 2.538 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1783 ; 3.763 ; 4.500 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B C D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 147 5 REMARK 3 1 B 1 B 147 5 REMARK 3 1 C 1 C 147 5 REMARK 3 1 D 1 D 147 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 588 ; 0.35 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 B (A): 588 ; 0.43 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 C (A): 588 ; 0.44 ; 0.50 REMARK 3 MEDIUM POSITIONAL 1 D (A): 588 ; 0.29 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 586 ; 1.01 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 B (A): 586 ; 0.96 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 C (A): 586 ; 0.98 ; 5.00 REMARK 3 LOOSE POSITIONAL 1 D (A): 586 ; 0.92 ; 5.00 REMARK 3 MEDIUM THERMAL 1 A (A**2): 588 ; 1.34 ; 2.00 REMARK 3 MEDIUM THERMAL 1 B (A**2): 588 ; 1.99 ; 2.00 REMARK 3 MEDIUM THERMAL 1 C (A**2): 588 ; 1.83 ; 2.00 REMARK 3 MEDIUM THERMAL 1 D (A**2): 588 ; 2.02 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 586 ; 2.16 ; 10.00 REMARK 3 LOOSE THERMAL 1 B (A**2): 586 ; 2.93 ; 10.00 REMARK 3 LOOSE THERMAL 1 C (A**2): 586 ; 2.75 ; 10.00 REMARK 3 LOOSE THERMAL 1 D (A**2): 586 ; 2.49 ; 10.00 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 1X23 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-APR-05. REMARK 100 THE RCSB ID CODE IS RCSB024281.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-04 REMARK 200 TEMPERATURE (KELVIN) : 100 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) : 0.900 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : BRUKER DIP-6040 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46077 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.24900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1QCQ REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES-NA, 10% ISO-PROPANOL, REMARK 280 20% PEG4000, PH 7.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 288K
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 22.16700 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 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 350 REMARK 350 BIOMOLECULE: 2 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: 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 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 -8 REMARK 465 PRO A -7 REMARK 465 GLY B -8 REMARK 465 PRO B -7 REMARK 465 LEU B -6 REMARK 465 GLY C -8 REMARK 465 PRO C -7 REMARK 465 LEU C -6 REMARK 465 GLY D -8
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 ILE B 137 O HOH B 284 1.80 REMARK 500 OD1 ASP B 116 O HOH B 311 1.84 REMARK 500 O ARG B 136 O HOH B 285 1.89 REMARK 500 N ARG B 136 O HOH B 301 1.92 REMARK 500 N GLU B 140 O HOH B 284 1.95 REMARK 500 O ILE B 123 O HOH B 172 1.98 REMARK 500 O HOH C 216 O HOH C 270 2.01 REMARK 500 NH1 ARG A 72 O HOH A 282 2.05 REMARK 500 O ARG B 139 O HOH B 286 2.06 REMARK 500 O GLY B 39 O HOH B 323 2.06 REMARK 500 O ASP B 132 O HOH B 301 2.07 REMARK 500 O HOH A 158 O HOH A 280 2.08 REMARK 500 O HOH A 286 O HOH D 237 2.10 REMARK 500 O HOH A 159 O HOH D 255 2.13 REMARK 500 O HOH A 173 O HOH A 314 2.13 REMARK 500 OXT MET A 147 O HOH A 290 2.15 REMARK 500 O HOH D 194 O HOH D 220 2.16 REMARK 500 OD2 ASP D 29 O HOH D 206 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 PHE A -1 C MET A 1 N 0.305 REMARK 500 PHE B -1 C MET B 1 N 0.282 REMARK 500 PHE C -1 C MET C 1 N 0.278 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 PHE C -1 O - C - N ANGL. DEV. = -10.6 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 ASP A 28 17.18 59.68 REMARK 500 PRO A 44 6.47 -69.87 REMARK 500 ARG A 90 -113.73 -108.30 REMARK 500 ASP B 42 24.41 93.58 REMARK 500 SER B 43 -40.10 -168.19 REMARK 500 ARG B 90 -99.15 -114.16 REMARK 500 PRO C -3 -1.04 -59.26 REMARK 500 GLN C 20 -15.11 84.32 REMARK 500 ARG C 90 -92.78 -111.49 REMARK 500 ALA D 19 -142.11 45.53 REMARK 500 GLN D 20 67.56 -104.16 REMARK 500 ARG D 90 -113.17 -112.85 REMARK 500 ASP D 117 73.50 -113.14 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 D 203 DISTANCE = 5.34 ANGSTROMS REMARK 525 HOH A 218 DISTANCE = 5.60 ANGSTROMS REMARK 525 HOH C 252 DISTANCE = 5.24 ANGSTROMS REMARK 525 HOH A 256 DISTANCE = 5.40 ANGSTROMS REMARK 525 HOH D 258 DISTANCE = 6.42 ANGSTROMS REMARK 525 HOH D 273 DISTANCE = 8.67 ANGSTROMS REMARK 525 HOH C 275 DISTANCE = 9.01 ANGSTROMS REMARK 525 HOH D 275 DISTANCE = 5.00 ANGSTROMS REMARK 525 HOH D 276 DISTANCE = 7.00 ANGSTROMS REMARK 525 HOH D 279 DISTANCE = 5.65 ANGSTROMS REMARK 525 HOH C 284 DISTANCE = 5.14 ANGSTROMS REMARK 525 HOH C 285 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH C 287 DISTANCE = 6.40 ANGSTROMS REMARK 525 HOH A 288 DISTANCE = 5.64 ANGSTROMS REMARK 525 HOH C 288 DISTANCE = 10.32 ANGSTROMS REMARK 525 HOH A 289 DISTANCE = 6.93 ANGSTROMS REMARK 525 HOH C 291 DISTANCE = 6.20 ANGSTROMS REMARK 525 HOH C 292 DISTANCE = 8.32 ANGSTROMS REMARK 525 HOH C 293 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH B 298 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH C 301 DISTANCE = 5.26 ANGSTROMS REMARK 525 HOH B 307 DISTANCE = 8.10 ANGSTROMS REMARK 525 HOH A 308 DISTANCE = 5.07 ANGSTROMS REMARK 525 HOH C 319 DISTANCE = 5.17 ANGSTROMS REMARK 525 HOH C 320 DISTANCE = 5.35 ANGSTROMS
DBREF 1X23 A 1 147 UNP P61077 UB2D3_HUMAN 1 147 DBREF 1X23 B 1 147 UNP P61077 UB2D3_HUMAN 1 147 DBREF 1X23 C 1 147 UNP P61077 UB2D3_HUMAN 1 147 DBREF 1X23 D 1 147 UNP P61077 UB2D3_HUMAN 1 147
SEQADV 1X23 GLY A -8 UNP P61077 CLONING ARTIFACT SEQADV 1X23 PRO A -7 UNP P61077 CLONING ARTIFACT SEQADV 1X23 LEU A -6 UNP P61077 CLONING ARTIFACT SEQADV 1X23 GLY A -5 UNP P61077 CLONING ARTIFACT SEQADV 1X23 SER A -4 UNP P61077 CLONING ARTIFACT SEQADV 1X23 PRO A -3 UNP P61077 CLONING ARTIFACT SEQADV 1X23 GLU A -2 UNP P61077 CLONING ARTIFACT SEQADV 1X23 PHE A -1 UNP P61077 CLONING ARTIFACT SEQADV 1X23 GLY B -8 UNP P61077 CLONING ARTIFACT SEQADV 1X23 PRO B -7 UNP P61077 CLONING ARTIFACT SEQADV 1X23 LEU B -6 UNP P61077 CLONING ARTIFACT SEQADV 1X23 GLY B -5 UNP P61077 CLONING ARTIFACT SEQADV 1X23 SER B -4 UNP P61077 CLONING ARTIFACT SEQADV 1X23 PRO B -3 UNP P61077 CLONING ARTIFACT SEQADV 1X23 GLU B -2 UNP P61077 CLONING ARTIFACT SEQADV 1X23 PHE B -1 UNP P61077 CLONING ARTIFACT SEQADV 1X23 GLY C -8 UNP P61077 CLONING ARTIFACT SEQADV 1X23 PRO C -7 UNP P61077 CLONING ARTIFACT SEQADV 1X23 LEU C -6 UNP P61077 CLONING ARTIFACT SEQADV 1X23 GLY C -5 UNP P61077 CLONING ARTIFACT SEQADV 1X23 SER C -4 UNP P61077 CLONING ARTIFACT SEQADV 1X23 PRO C -3 UNP P61077 CLONING ARTIFACT SEQADV 1X23 GLU C -2 UNP P61077 CLONING ARTIFACT SEQADV 1X23 PHE C -1 UNP P61077 CLONING ARTIFACT SEQADV 1X23 GLY D -8 UNP P61077 CLONING ARTIFACT SEQADV 1X23 PRO D -7 UNP P61077 CLONING ARTIFACT SEQADV 1X23 LEU D -6 UNP P61077 CLONING ARTIFACT SEQADV 1X23 GLY D -5 UNP P61077 CLONING ARTIFACT SEQADV 1X23 SER D -4 UNP P61077 CLONING ARTIFACT SEQADV 1X23 PRO D -3 UNP P61077 CLONING ARTIFACT SEQADV 1X23 GLU D -2 UNP P61077 CLONING ARTIFACT SEQADV 1X23 PHE D -1 UNP P61077 CLONING ARTIFACT
SEQRES 1 A 155 GLY PRO LEU GLY SER PRO GLU PHE MET ALA LEU LYS ARG SEQRES 2 A 155 ILE ASN LYS GLU LEU SER ASP LEU ALA ARG ASP PRO PRO SEQRES 3 A 155 ALA GLN CYS SER ALA GLY PRO VAL GLY ASP ASP MET PHE SEQRES 4 A 155 HIS TRP GLN ALA THR ILE MET GLY PRO ASN ASP SER PRO SEQRES 5 A 155 TYR GLN GLY GLY VAL PHE PHE LEU THR ILE HIS PHE PRO SEQRES 6 A 155 THR ASP TYR PRO PHE LYS PRO PRO LYS VAL ALA PHE THR SEQRES 7 A 155 THR ARG ILE TYR HIS PRO ASN ILE ASN SER ASN GLY SER SEQRES 8 A 155 ILE CYS LEU ASP ILE LEU ARG SER GLN TRP SER PRO ALA SEQRES 9 A 155 LEU THR ILE SER LYS VAL LEU LEU SER ILE CYS SER LEU SEQRES 10 A 155 LEU CYS ASP PRO ASN PRO ASP ASP PRO LEU VAL PRO GLU SEQRES 11 A 155 ILE ALA ARG ILE TYR LYS THR ASP ARG ASP LYS TYR ASN SEQRES 12 A 155 ARG ILE SER ARG GLU TRP THR GLN LYS TYR ALA MET SEQRES 1 B 155 GLY PRO LEU GLY SER PRO GLU PHE MET ALA LEU LYS ARG SEQRES 2 B 155 ILE ASN LYS GLU LEU SER ASP LEU ALA ARG ASP PRO PRO SEQRES 3 B 155 ALA GLN CYS SER ALA GLY PRO VAL GLY ASP ASP MET PHE SEQRES 4 B 155 HIS TRP GLN ALA THR ILE MET GLY PRO ASN ASP SER PRO SEQRES 5 B 155 TYR GLN GLY GLY VAL PHE PHE LEU THR ILE HIS PHE PRO SEQRES 6 B 155 THR ASP TYR PRO PHE LYS PRO PRO LYS VAL ALA PHE THR SEQRES 7 B 155 THR ARG ILE TYR HIS PRO ASN ILE ASN SER ASN GLY SER SEQRES 8 B 155 ILE CYS LEU ASP ILE LEU ARG SER GLN TRP SER PRO ALA SEQRES 9 B 155 LEU THR ILE SER LYS VAL LEU LEU SER ILE CYS SER LEU SEQRES 10 B 155 LEU CYS ASP PRO ASN PRO ASP ASP PRO LEU VAL PRO GLU SEQRES 11 B 155 ILE ALA ARG ILE TYR LYS THR ASP ARG ASP LYS TYR ASN SEQRES 12 B 155 ARG ILE SER ARG GLU TRP THR GLN LYS TYR ALA MET SEQRES 1 C 155 GLY PRO LEU GLY SER PRO GLU PHE MET ALA LEU LYS ARG SEQRES 2 C 155 ILE ASN LYS GLU LEU SER ASP LEU ALA ARG ASP PRO PRO SEQRES 3 C 155 ALA GLN CYS SER ALA GLY PRO VAL GLY ASP ASP MET PHE SEQRES 4 C 155 HIS TRP GLN ALA THR ILE MET GLY PRO ASN ASP SER PRO SEQRES 5 C 155 TYR GLN GLY GLY VAL PHE PHE LEU THR ILE HIS PHE PRO SEQRES 6 C 155 THR ASP TYR PRO PHE LYS PRO PRO LYS VAL ALA PHE THR SEQRES 7 C 155 THR ARG ILE TYR HIS PRO ASN ILE ASN SER ASN GLY SER SEQRES 8 C 155 ILE CYS LEU ASP ILE LEU ARG SER GLN TRP SER PRO ALA SEQRES 9 C 155 LEU THR ILE SER LYS VAL LEU LEU SER ILE CYS SER LEU SEQRES 10 C 155 LEU CYS ASP PRO ASN PRO ASP ASP PRO LEU VAL PRO GLU SEQRES 11 C 155 ILE ALA ARG ILE TYR LYS THR ASP ARG ASP LYS TYR ASN SEQRES 12 C 155 ARG ILE SER ARG GLU TRP THR GLN LYS TYR ALA MET SEQRES 1 D 155 GLY PRO LEU GLY SER PRO GLU PHE MET ALA LEU LYS ARG SEQRES 2 D 155 ILE ASN LYS GLU LEU SER ASP LEU ALA ARG ASP PRO PRO SEQRES 3 D 155 ALA GLN CYS SER ALA GLY PRO VAL GLY ASP ASP MET PHE SEQRES 4 D 155 HIS TRP GLN ALA THR ILE MET GLY PRO ASN ASP SER PRO SEQRES 5 D 155 TYR GLN GLY GLY VAL PHE PHE LEU THR ILE HIS PHE PRO SEQRES 6 D 155 THR ASP TYR PRO PHE LYS PRO PRO LYS VAL ALA PHE THR SEQRES 7 D 155 THR ARG ILE TYR HIS PRO ASN ILE ASN SER ASN GLY SER SEQRES 8 D 155 ILE CYS LEU ASP ILE LEU ARG SER GLN TRP SER PRO ALA SEQRES 9 D 155 LEU THR ILE SER LYS VAL LEU LEU SER ILE CYS SER LEU SEQRES 10 D 155 LEU CYS ASP PRO ASN PRO ASP ASP PRO LEU VAL PRO GLU SEQRES 11 D 155 ILE ALA ARG ILE TYR LYS THR ASP ARG ASP LYS TYR ASN SEQRES 12 D 155 ARG ILE SER ARG GLU TRP THR GLN LYS TYR ALA MET
FORMUL 5 HOH *677(H2 O)
HELIX 1 1 GLU A -2 ASP A 16 1 18 HELIX 2 2 LEU A 86 ARG A 90 5 5 HELIX 3 3 THR A 98 ASP A 112 1 15 HELIX 4 4 VAL A 120 ASP A 130 1 11 HELIX 5 5 ASP A 130 ALA A 146 1 17 HELIX 6 6 GLU B -2 ASP B 16 1 18 HELIX 7 7 LEU B 86 ARG B 90 5 5 HELIX 8 8 THR B 98 LEU B 110 1 13 HELIX 9 9 VAL B 120 ASP B 130 1 11 HELIX 10 10 ASP B 130 ALA B 146 1 17 HELIX 11 11 GLU C -2 ASP C 16 1 18 HELIX 12 12 LEU C 86 ARG C 90 5 5 HELIX 13 13 THR C 98 ASP C 112 1 15 HELIX 14 14 VAL C 120 ASP C 130 1 11 HELIX 15 15 ASP C 130 ALA C 146 1 17 HELIX 16 16 GLU D -2 PHE D -1 1 2 HELIX 17 17 MET D 1 ASP D 16 1 16 HELIX 18 18 LEU D 86 ARG D 90 5 5 HELIX 19 19 THR D 98 ASP D 112 1 15 HELIX 20 20 VAL D 120 ASP D 130 1 11 HELIX 21 21 ASP D 130 ALA D 146 1 17
SHEET 1 A 4 CYS A 21 PRO A 25 0 SHEET 2 A 4 HIS A 32 MET A 38 -1 O THR A 36 N SER A 22 SHEET 3 A 4 VAL A 49 HIS A 55 -1 O ILE A 54 N TRP A 33 SHEET 4 A 4 LYS A 66 PHE A 69 -1 O ALA A 68 N THR A 53 SHEET 1 B 4 CYS B 21 VAL B 26 0 SHEET 2 B 4 ASP B 29 MET B 38 -1 O GLN B 34 N GLY B 24 SHEET 3 B 4 VAL B 49 HIS B 55 -1 O PHE B 50 N ILE B 37 SHEET 4 B 4 LYS B 66 PHE B 69 -1 O LYS B 66 N HIS B 55 SHEET 1 C 4 CYS C 21 PRO C 25 0 SHEET 2 C 4 HIS C 32 MET C 38 -1 O GLN C 34 N GLY C 24 SHEET 3 C 4 VAL C 49 HIS C 55 -1 O ILE C 54 N TRP C 33 SHEET 4 C 4 LYS C 66 PHE C 69 -1 O LYS C 66 N HIS C 55 SHEET 1 D 4 CYS D 21 PRO D 25 0 SHEET 2 D 4 HIS D 32 MET D 38 -1 O THR D 36 N SER D 22 SHEET 3 D 4 VAL D 49 HIS D 55 -1 O PHE D 50 N ILE D 37 SHEET 4 D 4 LYS D 66 PHE D 69 -1 O LYS D 66 N HIS D 55
SSBOND 1 CYS A 21 CYS A 107 1555 1555 2.95
CISPEP 1 TYR A 60 PRO A 61 0 2.60 CISPEP 2 PRO B 40 ASN B 41 0 -24.96 CISPEP 3 ASN B 41 ASP B 42 0 -19.01 CISPEP 4 ASP B 42 SER B 43 0 10.66 CISPEP 5 TYR B 60 PRO B 61 0 5.91 CISPEP 6 TYR C 60 PRO C 61 0 9.11 CISPEP 7 PRO D -7 LEU D -6 0 -11.17 CISPEP 8 TYR D 60 PRO D 61 0 3.04
CRYST1 61.998 44.334 97.584 90.00 93.36 90.00 P 1 21 1 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 0.016130 0.000000 0.000948 0.00000
SCALE2 0.000000 0.022556 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010265 0.00000