HEADER CELL CYCLE/PROTEIN BINDING 17-MAY-12 4F8C TITLE STRUCTURE OF THE CIF:NEDD8 COMPLEX - YERSINIA PSEUDOTUBERCULOSIS CYCLE TITLE 2 INHIBITING FACTOR IN COMPLEX WITH HUMAN NEDD8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLE INHIBITING FACTOR; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: EFFECTOR DOMAIN, UNP RESIDUES 33-288; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NEDD8; COMPND 9 CHAIN: B, D; COMPND 10 SYNONYM: NEDDYLIN, NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY COMPND 11 DOWN-REGULATED PROTEIN 8, NEDD-8, UBIQUITIN-LIKE PROTEIN NEDD8; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PSEUDOTUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 502800; SOURCE 4 STRAIN: YPIII; SOURCE 5 GENE: YPK_1971; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SOLUBL21; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: NEDD8; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) ROSSETTA KEYWDS EFFECTOR-HOST TARGET COMPLEX, GLUTAMINE DEAMIDASE, DEAMIDATION, KEYWDS 2 BACTERIAL EFFECTOR, CELL CYCLE-PROTEIN BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.CROW,M.BANFIELD REVDAT 1 20-JUN-12 4F8C 0 JRNL AUTH A.CROW,R.K.HUGHES,F.TAIEB,E.OSWALD,M.J.BANFIELD JRNL TITL THE MOLECULAR BASIS OF NEDD8 DEAMIDATION BY THE BACTERIAL JRNL TITL 2 EFFECTOR PROTEIN CIF JRNL REF PROC.NATL.ACAD.SCI.USA 2012 JRNL REFN ESSN 1091-6490 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0025 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.81 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 54900 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2938 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3972 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.81 REMARK 3 BIN R VALUE (WORKING SET) : 0.2230 REMARK 3 BIN FREE R VALUE SET COUNT : 221 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5097 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 318 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.35 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : -0.14000 REMARK 3 B12 (A**2) : 0.05000 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): 0.157 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5543 ; 0.025 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7530 ; 1.950 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 709 ; 6.682 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 267 ;38.587 ;25.169 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1024 ;16.039 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 32 ;18.770 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 855 ; 0.152 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4220 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED 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: NULL REMARK 4 REMARK 4 4F8C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-MAY-12. REMARK 100 THE RCSB ID CODE IS RCSB072582. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-11 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 : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00720 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57931 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 66.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07900 REMARK 200 FOR THE DATA SET : 18.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.46300 REMARK 200 FOR SHELL : 4.200 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 ENTRY 4FBJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.2M SODIUM MALONATE, 44MM BIS-TRIS REMARK 280 PROPANE (PH 7.0), 66MM BIS-TRIS PROPANE (PH 8.0), VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 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 REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 -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 0.00000 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 0.00000 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 84.96500 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 84.96500 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 84.96500 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 0.00000 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 0.00000 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 84.96500 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 84.96500 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 84.96500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 MET A 14 REMARK 465 ALA A 15 REMARK 465 HIS A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 HIS A 19 REMARK 465 HIS A 20 REMARK 465 HIS A 21 REMARK 465 SER A 22 REMARK 465 SER A 23 REMARK 465 GLY A 24 REMARK 465 LEU A 25 REMARK 465 GLU A 26 REMARK 465 VAL A 27 REMARK 465 LEU A 28 REMARK 465 PHE A 29 REMARK 465 GLN A 30 REMARK 465 GLY A 31 REMARK 465 PRO A 32 REMARK 465 PRO A 33 REMARK 465 VAL A 34 REMARK 465 SER A 35 REMARK 465 HIS A 36 REMARK 465 SER A 37 REMARK 465 ILE A 38 REMARK 465 ASN A 39 REMARK 465 GLY B 75 REMARK 465 GLY B 76 REMARK 465 GLY B 77 REMARK 465 GLY B 78 REMARK 465 LEU B 79 REMARK 465 ARG B 80 REMARK 465 GLN B 81 REMARK 465 LYS B 82 REMARK 465 HIS B 83 REMARK 465 HIS B 84 REMARK 465 HIS B 85 REMARK 465 HIS B 86 REMARK 465 HIS B 87 REMARK 465 HIS B 88 REMARK 465 MET C 14 REMARK 465 ALA C 15 REMARK 465 HIS C 16 REMARK 465 HIS C 17 REMARK 465 HIS C 18 REMARK 465 HIS C 19 REMARK 465 HIS C 20 REMARK 465 HIS C 21 REMARK 465 SER C 22 REMARK 465 SER C 23 REMARK 465 GLY C 24 REMARK 465 LEU C 25 REMARK 465 GLU C 26 REMARK 465 VAL C 27 REMARK 465 LEU C 28 REMARK 465 PHE C 29 REMARK 465 GLN C 30 REMARK 465 GLY C 31 REMARK 465 PRO C 32 REMARK 465 PRO C 33 REMARK 465 VAL C 34 REMARK 465 SER C 35 REMARK 465 HIS C 36 REMARK 465 SER C 37 REMARK 465 ILE C 38 REMARK 465 ASN C 39 REMARK 465 HIS C 288 REMARK 465 ARG D 74 REMARK 465 GLY D 75 REMARK 465 GLY D 76 REMARK 465 GLY D 77 REMARK 465 GLY D 78 REMARK 465 LEU D 79 REMARK 465 ARG D 80 REMARK 465 GLN D 81 REMARK 465 LYS D 82 REMARK 465 HIS D 83 REMARK 465 HIS D 84 REMARK 465 HIS D 85 REMARK 465 HIS D 86 REMARK 465 HIS D 87 REMARK 465 HIS D 88 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 OG SER A 143 O HOH A 433 1.89 REMARK 500 OD1 ASP C 222 O HOH C 463 2.09 REMARK 500 OE1 GLU C 139 O HOH C 428 2.13 REMARK 500 O HOH C 479 O HOH C 480 2.19 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 ARG A 205 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 PRO C 41 C - N - CA ANGL. DEV. = -12.4 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 ASN A 131 -166.04 -160.56 REMARK 500 PHE A 179 79.54 -113.45 REMARK 500 LYS A 286 -7.68 -58.21 REMARK 500 SER B 46 77.92 42.79 REMARK 500 ASN C 131 -157.89 -161.20 REMARK 500 PRO C 185 -38.19 -34.20 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN C 40 18.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO C 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4FBJ RELATED DB: PDB DBREF 4F8C A 33 288 UNP B1JJZ9 B1JJZ9_YERPY 33 288 DBREF 4F8C B 1 81 UNP Q15843 NEDD8_HUMAN 1 81 DBREF 4F8C C 33 288 UNP B1JJZ9 B1JJZ9_YERPY 33 288 DBREF 4F8C D 1 81 UNP Q15843 NEDD8_HUMAN 1 81 SEQADV 4F8C MET A 14 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C ALA A 15 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C HIS A 16 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C HIS A 17 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C HIS A 18 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C HIS A 19 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C HIS A 20 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C HIS A 21 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C SER A 22 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C SER A 23 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C GLY A 24 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C LEU A 25 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C GLU A 26 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C VAL A 27 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C LEU A 28 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C PHE A 29 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C GLN A 30 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C GLY A 31 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C PRO A 32 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C ALA A 117 UNP B1JJZ9 CYS 117 ENGINEERED MUTATION SEQADV 4F8C LYS B 82 UNP Q15843 EXPRESSION TAG SEQADV 4F8C HIS B 83 UNP Q15843 EXPRESSION TAG SEQADV 4F8C HIS B 84 UNP Q15843 EXPRESSION TAG SEQADV 4F8C HIS B 85 UNP Q15843 EXPRESSION TAG SEQADV 4F8C HIS B 86 UNP Q15843 EXPRESSION TAG SEQADV 4F8C HIS B 87 UNP Q15843 EXPRESSION TAG SEQADV 4F8C HIS B 88 UNP Q15843 EXPRESSION TAG SEQADV 4F8C MET C 14 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C ALA C 15 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C HIS C 16 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C HIS C 17 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C HIS C 18 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C HIS C 19 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C HIS C 20 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C HIS C 21 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C SER C 22 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C SER C 23 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C GLY C 24 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C LEU C 25 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C GLU C 26 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C VAL C 27 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C LEU C 28 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C PHE C 29 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C GLN C 30 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C GLY C 31 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C PRO C 32 UNP B1JJZ9 EXPRESSION TAG SEQADV 4F8C ALA C 117 UNP B1JJZ9 CYS 117 ENGINEERED MUTATION SEQADV 4F8C LYS D 82 UNP Q15843 EXPRESSION TAG SEQADV 4F8C HIS D 83 UNP Q15843 EXPRESSION TAG SEQADV 4F8C HIS D 84 UNP Q15843 EXPRESSION TAG SEQADV 4F8C HIS D 85 UNP Q15843 EXPRESSION TAG SEQADV 4F8C HIS D 86 UNP Q15843 EXPRESSION TAG SEQADV 4F8C HIS D 87 UNP Q15843 EXPRESSION TAG SEQADV 4F8C HIS D 88 UNP Q15843 EXPRESSION TAG SEQRES 1 A 275 MET ALA HIS HIS HIS HIS HIS HIS SER SER GLY LEU GLU SEQRES 2 A 275 VAL LEU PHE GLN GLY PRO PRO VAL SER HIS SER ILE ASN SEQRES 3 A 275 ASN PRO SER ILE GLN HIS VAL GLN ASP PHE ALA THR LEU SEQRES 4 A 275 SER ALA ARG SER LEU ARG ALA ASN VAL LEU LEU ASN SER SEQRES 5 A 275 ASP ASP HIS SER VAL PRO ILE HIS ALA LYS ASN PRO SER SEQRES 6 A 275 GLU LEU LEU GLU ALA ILE ASP ASN ASN ILE SER GLN THR SEQRES 7 A 275 ALA GLN ASP TRP GLY VAL SER ILE GLN GLU VAL GLU VAL SEQRES 8 A 275 ILE LEU GLY SER SER LYS ARG ILE ILE GLU PRO VAL ALA SEQRES 9 A 275 GLY VAL THR ALA ASN THR ILE MET LYS LEU PHE LEU ASP SEQRES 10 A 275 ASN ASP ILE PHE SER TYR SER PHE GLU LYS GLY GLN SER SEQRES 11 A 275 LEU SER LEU SER GLN LEU GLN GLU ARG LEU ALA SER LEU SEQRES 12 A 275 PRO ALA HIS LYS ASN PHE ILE LEU ARG VAL ASN ASP GLY SEQRES 13 A 275 GLY LEU GLY HIS ALA TYR VAL ILE ASP PHE PRO ALA THR SEQRES 14 A 275 THR ASN PRO SER ARG ASP ALA PHE LEU TYR GLN SER ASP SEQRES 15 A 275 LEU GLY GLU GLY VAL THR ARG GLU VAL ARG PHE GLU ASP SEQRES 16 A 275 TRP MET THR GLN LYS ALA SER HIS PRO ILE SER LEU ASP SEQRES 17 A 275 ASP ILE ASN THR HIS PHE ILE GLY ILE ALA GLN ASP GLN SEQRES 18 A 275 ILE ASP LEU ALA HIS ILE ALA LYS LEU PHE ASP VAL ASP SEQRES 19 A 275 GLY ASN VAL LYS MET LEU ARG ALA ASP HIS LEU ILE SER SEQRES 20 A 275 HIS LYS THR SER GLU PHE ASN PHE GLN LEU PHE GLU TYR SEQRES 21 A 275 ASP LEU LYS ASN LEU GLU ASN ASN MET SER ILE ILE LYS SEQRES 22 A 275 THR HIS SEQRES 1 B 88 MET LEU ILE LYS VAL LYS THR LEU THR GLY LYS GLU ILE SEQRES 2 B 88 GLU ILE ASP ILE GLU PRO THR ASP LYS VAL GLU ARG ILE SEQRES 3 B 88 LYS GLU ARG VAL GLU GLU LYS GLU GLY ILE PRO PRO GLN SEQRES 4 B 88 GLN GLN ARG LEU ILE TYR SER GLY LYS GLN MET ASN ASP SEQRES 5 B 88 GLU LYS THR ALA ALA ASP TYR LYS ILE LEU GLY GLY SER SEQRES 6 B 88 VAL LEU HIS LEU VAL LEU ALA LEU ARG GLY GLY GLY GLY SEQRES 7 B 88 LEU ARG GLN LYS HIS HIS HIS HIS HIS HIS SEQRES 1 C 275 MET ALA HIS HIS HIS HIS HIS HIS SER SER GLY LEU GLU SEQRES 2 C 275 VAL LEU PHE GLN GLY PRO PRO VAL SER HIS SER ILE ASN SEQRES 3 C 275 ASN PRO SER ILE GLN HIS VAL GLN ASP PHE ALA THR LEU SEQRES 4 C 275 SER ALA ARG SER LEU ARG ALA ASN VAL LEU LEU ASN SER SEQRES 5 C 275 ASP ASP HIS SER VAL PRO ILE HIS ALA LYS ASN PRO SER SEQRES 6 C 275 GLU LEU LEU GLU ALA ILE ASP ASN ASN ILE SER GLN THR SEQRES 7 C 275 ALA GLN ASP TRP GLY VAL SER ILE GLN GLU VAL GLU VAL SEQRES 8 C 275 ILE LEU GLY SER SER LYS ARG ILE ILE GLU PRO VAL ALA SEQRES 9 C 275 GLY VAL THR ALA ASN THR ILE MET LYS LEU PHE LEU ASP SEQRES 10 C 275 ASN ASP ILE PHE SER TYR SER PHE GLU LYS GLY GLN SER SEQRES 11 C 275 LEU SER LEU SER GLN LEU GLN GLU ARG LEU ALA SER LEU SEQRES 12 C 275 PRO ALA HIS LYS ASN PHE ILE LEU ARG VAL ASN ASP GLY SEQRES 13 C 275 GLY LEU GLY HIS ALA TYR VAL ILE ASP PHE PRO ALA THR SEQRES 14 C 275 THR ASN PRO SER ARG ASP ALA PHE LEU TYR GLN SER ASP SEQRES 15 C 275 LEU GLY GLU GLY VAL THR ARG GLU VAL ARG PHE GLU ASP SEQRES 16 C 275 TRP MET THR GLN LYS ALA SER HIS PRO ILE SER LEU ASP SEQRES 17 C 275 ASP ILE ASN THR HIS PHE ILE GLY ILE ALA GLN ASP GLN SEQRES 18 C 275 ILE ASP LEU ALA HIS ILE ALA LYS LEU PHE ASP VAL ASP SEQRES 19 C 275 GLY ASN VAL LYS MET LEU ARG ALA ASP HIS LEU ILE SER SEQRES 20 C 275 HIS LYS THR SER GLU PHE ASN PHE GLN LEU PHE GLU TYR SEQRES 21 C 275 ASP LEU LYS ASN LEU GLU ASN ASN MET SER ILE ILE LYS SEQRES 22 C 275 THR HIS SEQRES 1 D 88 MET LEU ILE LYS VAL LYS THR LEU THR GLY LYS GLU ILE SEQRES 2 D 88 GLU ILE ASP ILE GLU PRO THR ASP LYS VAL GLU ARG ILE SEQRES 3 D 88 LYS GLU ARG VAL GLU GLU LYS GLU GLY ILE PRO PRO GLN SEQRES 4 D 88 GLN GLN ARG LEU ILE TYR SER GLY LYS GLN MET ASN ASP SEQRES 5 D 88 GLU LYS THR ALA ALA ASP TYR LYS ILE LEU GLY GLY SER SEQRES 6 D 88 VAL LEU HIS LEU VAL LEU ALA LEU ARG GLY GLY GLY GLY SEQRES 7 D 88 LEU ARG GLN LYS HIS HIS HIS HIS HIS HIS HET EDO A 301 4 HET EDO A 302 4 HET EDO C 301 4 HET EDO C 302 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 EDO 4(C2 H6 O2) FORMUL 9 HOH *318(H2 O) HELIX 1 1 ASN A 40 ALA A 54 1 15 HELIX 2 2 SER A 56 ASN A 64 1 9 HELIX 3 3 PRO A 71 LYS A 75 5 5 HELIX 4 4 ASN A 76 GLY A 96 1 21 HELIX 5 5 SER A 98 GLY A 107 1 10 HELIX 6 6 VAL A 116 ASP A 130 1 15 HELIX 7 7 SER A 145 SER A 155 1 11 HELIX 8 8 ARG A 205 LYS A 213 1 9 HELIX 9 9 LEU A 220 ILE A 230 1 11 HELIX 10 10 ASP A 236 ASP A 245 1 10 HELIX 11 11 ASN A 249 LEU A 253 5 5 HELIX 12 12 ARG A 254 LEU A 258 5 5 HELIX 13 13 ILE A 259 THR A 263 5 5 HELIX 14 14 ASP A 274 LYS A 286 1 13 HELIX 15 15 LYS B 22 GLY B 35 1 14 HELIX 16 16 PRO B 37 GLN B 41 5 5 HELIX 17 17 THR B 55 LYS B 60 1 6 HELIX 18 18 PRO C 41 ALA C 54 1 14 HELIX 19 19 SER C 56 ASN C 64 1 9 HELIX 20 20 PRO C 71 LYS C 75 5 5 HELIX 21 21 ASN C 76 GLY C 96 1 21 HELIX 22 22 SER C 98 GLY C 107 1 10 HELIX 23 23 VAL C 116 ASP C 130 1 15 HELIX 24 24 SER C 137 GLY C 141 5 5 HELIX 25 25 SER C 145 ALA C 154 1 10 HELIX 26 26 ARG C 205 LYS C 213 1 9 HELIX 27 27 SER C 219 GLN C 232 1 14 HELIX 28 28 ASP C 236 ASP C 245 1 10 HELIX 29 29 ASN C 249 LEU C 253 5 5 HELIX 30 30 ARG C 254 LEU C 258 5 5 HELIX 31 31 ILE C 259 THR C 263 5 5 HELIX 32 32 ASP C 274 LYS C 286 1 13 HELIX 33 33 LYS D 22 GLY D 35 1 14 HELIX 34 34 PRO D 37 GLN D 41 5 5 HELIX 35 35 ALA D 56 LYS D 60 5 5 SHEET 1 A 5 ILE A 218 SER A 219 0 SHEET 2 A 5 ASP A 188 TYR A 192 -1 N ALA A 189 O ILE A 218 SHEET 3 A 5 HIS A 173 PHE A 179 -1 N VAL A 176 O TYR A 192 SHEET 4 A 5 ASN A 161 ASP A 168 -1 N PHE A 162 O PHE A 179 SHEET 5 A 5 PHE A 266 TYR A 273 -1 O GLN A 269 N ARG A 165 SHEET 1 B 5 GLU B 12 ASP B 16 0 SHEET 2 B 5 LEU B 2 LYS B 6 -1 N VAL B 5 O ILE B 13 SHEET 3 B 5 VAL B 66 VAL B 70 1 O LEU B 67 N LYS B 6 SHEET 4 B 5 ARG B 42 TYR B 45 -1 N ARG B 42 O VAL B 70 SHEET 5 B 5 LYS B 48 GLN B 49 -1 O LYS B 48 N TYR B 45 SHEET 1 C 4 PHE C 190 TYR C 192 0 SHEET 2 C 4 HIS C 173 PHE C 179 -1 N VAL C 176 O TYR C 192 SHEET 3 C 4 ASN C 161 ASP C 168 -1 N PHE C 162 O PHE C 179 SHEET 4 C 4 PHE C 266 TYR C 273 -1 O GLN C 269 N ARG C 165 SHEET 1 D 5 GLU D 12 ASP D 16 0 SHEET 2 D 5 LEU D 2 LYS D 6 -1 N VAL D 5 O ILE D 13 SHEET 3 D 5 VAL D 66 VAL D 70 1 O LEU D 69 N LYS D 6 SHEET 4 D 5 ARG D 42 TYR D 45 -1 N ARG D 42 O VAL D 70 SHEET 5 D 5 LYS D 48 GLN D 49 -1 O LYS D 48 N TYR D 45 SITE 1 AC1 7 LEU A 57 ASN A 60 VAL A 61 SER A 108 SITE 2 AC1 7 SER A 109 ARG A 111 HOH A 510 SITE 1 AC2 6 HIS A 226 GLY A 229 ILE A 235 ASP A 236 SITE 2 AC2 6 HIS A 239 ILE A 240 SITE 1 AC3 6 THR C 225 HIS C 226 ILE C 235 ASP C 236 SITE 2 AC3 6 HIS C 239 ILE C 240 SITE 1 AC4 6 LEU C 57 ASN C 60 VAL C 61 SER C 108 SITE 2 AC4 6 ARG C 111 HOH C 530 CRYST1 125.359 125.359 169.930 90.00 90.00 120.00 P 63 2 2 24 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 0.007977 0.004606 0.000000 0.00000 SCALE2 0.000000 0.009211 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005885 0.00000 MASTER 456 0 4 35 19 0 8 6 0 0 0 58 END