HEADER CELL CYCLE/PROTEIN BINDING 23-MAY-12 4FBJ TITLE STRUCTURE OF THE CIF:NEDD8 COMPLEX - PHOTORHABDUS LUMINESCENS CYCLE TITLE 2 INHIBITING FACTOR IN COMPLEX WITH HUMAN NEDD8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EFFECTOR DOMAIN, UNP RESIDUES 53-313; COMPND 5 SYNONYM: CIF; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: NEDD8; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: NEDDYLIN, NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY COMPND 12 DOWN-REGULATED PROTEIN 8, NEDD-8, UBIQUITIN-LIKE PROTEIN NEDD8; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHOTORHABDUS LUMINESCENS SUBSP. LAUMONDII; SOURCE 3 ORGANISM_TAXID: 243265; SOURCE 4 STRAIN: TT01; SOURCE 5 GENE: PLU2515; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); 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: ROSSETTA (DE3) 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.J.BANFIELD REVDAT 2 08-NOV-23 4FBJ 1 REMARK SEQADV REVDAT 1 20-JUN-12 4FBJ 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. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 38.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.9 REMARK 3 NUMBER OF REFLECTIONS : 35599 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1881 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) : 2634 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.2630 REMARK 3 BIN FREE R VALUE SET COUNT : 120 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2586 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 376 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.21000 REMARK 3 B22 (A**2) : -0.46000 REMARK 3 B33 (A**2) : 0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.43000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.146 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.116 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.185 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2829 ; 0.024 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3850 ; 2.047 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 366 ; 6.873 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;37.814 ;25.942 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 551 ;14.651 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;16.983 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 429 ; 0.143 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2167 ; 0.010 ; 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): 1742 ; 2.413 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2853 ; 3.628 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1087 ; 5.333 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 997 ; 7.642 ; 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): 2417 ; 2.829 ; 3.000 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 : 1.40 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 4FBJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1000072695. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I02 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91340 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39093 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 42.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05200 REMARK 200 FOR THE DATA SET : 11.5000 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) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28800 REMARK 200 FOR SHELL : 3.000 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 3GQJ AND 1NDD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.77 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4000, 200MM SODIUM ACETATE, REMARK 280 100MM MES PH 6.7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K 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 28.04500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 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 LYS A 48 REMARK 465 ASN A 49 REMARK 465 SER A 50 REMARK 465 ASP A 301 REMARK 465 LYS A 302 REMARK 465 LYS A 303 REMARK 465 LEU A 304 REMARK 465 SER A 305 REMARK 465 LYS A 306 REMARK 465 PRO A 307 REMARK 465 LYS A 308 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 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 TYR B 59 O HOH B 188 1.88 REMARK 500 ND2 ASN A 89 O HOH A 733 2.07 REMARK 500 ND1 HIS A 257 O HOH A 519 2.08 REMARK 500 OD1 ASN A 89 O HOH A 718 2.10 REMARK 500 NH1 ARG A 272 O HOH A 556 2.10 REMARK 500 OE2 GLU A 193 O HOH A 772 2.12 REMARK 500 O HOH A 743 O HOH A 747 2.15 REMARK 500 O HOH B 119 O HOH B 179 2.16 REMARK 500 NH1 ARG B 29 O HOH B 150 2.16 REMARK 500 OE2 GLU A 100 O HOH A 704 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 776 O HOH B 118 2556 2.01 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 ASP A 95 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 247 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 LEU B 8 CB - CG - CD1 ANGL. DEV. = -10.7 DEGREES REMARK 500 ARG B 29 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 29 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 MET B 50 CG - SD - CE ANGL. DEV. = -15.2 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 GLU A 193 114.03 -174.83 REMARK 500 SER A 219 -54.30 -129.43 REMARK 500 LYS A 258 45.65 36.19 REMARK 500 LYS A 258 45.65 70.20 REMARK 500 SER B 46 70.81 25.16 REMARK 500 LEU B 71 46.50 -99.34 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 TYR B 45 SER B 46 -127.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE LIGAND IN THE STRUCTURE IS AN UNKNOWN ATOM OR ION WHICH MAY REMARK 600 PROBABABLY BE AN CHLORIDE, AND WAS REFINED AS CL A 401. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4F8C RELATED DB: PDB REMARK 900 CIF:NEDD8 COMPLEX FROM YERSINIA PSEUDOTUBERCULOSIS DBREF 4FBJ A 48 308 UNP Q7N439 Q7N439_PHOLL 53 313 DBREF 4FBJ B 1 81 UNP Q15843 NEDD8_HUMAN 1 81 SEQADV 4FBJ SER A 123 UNP Q7N439 CYS 128 ENGINEERED MUTATION SEQADV 4FBJ LYS B 82 UNP Q15843 EXPRESSION TAG SEQADV 4FBJ HIS B 83 UNP Q15843 EXPRESSION TAG SEQADV 4FBJ HIS B 84 UNP Q15843 EXPRESSION TAG SEQADV 4FBJ HIS B 85 UNP Q15843 EXPRESSION TAG SEQADV 4FBJ HIS B 86 UNP Q15843 EXPRESSION TAG SEQADV 4FBJ HIS B 87 UNP Q15843 EXPRESSION TAG SEQADV 4FBJ HIS B 88 UNP Q15843 EXPRESSION TAG SEQRES 1 A 261 LYS ASN SER ILE ASN THR ILE LYS LEU ILE ASP ASP ILE SEQRES 2 A 261 ILE ALA LEU HIS ASN ASP PRO LYS GLY ASN LYS LEU LEU SEQRES 3 A 261 TRP ASN ASP ASN TRP GLN ASP LYS ILE ILE ASN ARG ASP SEQRES 4 A 261 LEU ALA ASN ILE PHE GLU LYS ILE ASP GLU SER VAL SER SEQRES 5 A 261 GLU LEU GLY GLY LEU GLU MET TYR GLN GLU MET VAL GLY SEQRES 6 A 261 VAL ASN PRO TYR ASP PRO THR GLU PRO VAL SER GLY LEU SEQRES 7 A 261 SER ALA GLN ASN ILE PHE LYS LEU MET THR GLU GLY GLU SEQRES 8 A 261 HIS ALA VAL ASP PRO VAL GLU MET ALA GLN THR GLY LYS SEQRES 9 A 261 ILE ASP GLY ASN GLU PHE ALA GLU SER VAL ASP GLN LEU SEQRES 10 A 261 SER SER ALA LYS ASN TYR VAL ALA LEU VAL ASN ASP ARG SEQRES 11 A 261 ARG LEU GLY HIS MET PHE LEU ILE ASP ILE PRO SER ASN SEQRES 12 A 261 ASP GLN GLU THR VAL GLY TYR ILE TYR GLN SER ASP LEU SEQRES 13 A 261 GLY GLN GLY ALA LEU PRO PRO LEU LYS ILE ALA ASP TRP SEQRES 14 A 261 LEU ASN SER ARG GLY LYS ASP ALA VAL SER LEU ASN LYS SEQRES 15 A 261 LEU LYS LYS LEU LEU SER ARG GLU PHE ASN LEU LEU SER SEQRES 16 A 261 ASP ASP GLU LYS ARG ALA LEU ILE SER GLU THR LEU ASP SEQRES 17 A 261 ILE HIS LYS ASP VAL SER ASN VAL GLU LEU ASP ARG ILE SEQRES 18 A 261 LYS ARG ASP ARG GLY VAL ASP ILE TYR LEU THR GLU TYR SEQRES 19 A 261 ASP VAL ASN ASN PHE TYR GLU ASN ILE GLU THR LEU LYS SEQRES 20 A 261 SER LYS LEU SER ASN TYR ASP LYS LYS LEU SER LYS PRO SEQRES 21 A 261 LYS 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 HET CL A 401 1 HETNAM CL CHLORIDE ION FORMUL 3 CL CL 1- FORMUL 4 HOH *376(H2 O) HELIX 1 1 ASN A 52 ASP A 66 1 15 HELIX 2 2 ASP A 66 TRP A 74 1 9 HELIX 3 3 LYS A 81 ARG A 85 5 5 HELIX 4 4 ASP A 86 LEU A 101 1 16 HELIX 5 5 GLY A 103 GLY A 112 1 10 HELIX 6 6 VAL A 122 GLU A 136 1 15 HELIX 7 7 ASP A 142 GLY A 150 1 9 HELIX 8 8 ASP A 153 VAL A 161 1 9 HELIX 9 9 ASP A 162 LEU A 164 5 3 HELIX 10 10 LYS A 212 SER A 219 1 8 HELIX 11 11 ARG A 220 LYS A 222 5 3 HELIX 12 12 LEU A 227 SER A 235 1 9 HELIX 13 13 ARG A 236 LEU A 241 5 6 HELIX 14 14 SER A 242 ASP A 255 1 14 HELIX 15 15 ASP A 259 VAL A 263 5 5 HELIX 16 16 GLU A 264 ILE A 268 5 5 HELIX 17 17 ASP A 282 ASN A 299 1 18 HELIX 18 18 LYS B 22 GLY B 35 1 14 HELIX 19 19 PRO B 37 GLN B 41 5 5 SHEET 1 A 5 ALA A 224 SER A 226 0 SHEET 2 A 5 VAL A 195 TYR A 199 -1 N GLY A 196 O VAL A 225 SHEET 3 A 5 HIS A 181 ILE A 187 -1 N ASP A 186 O TYR A 197 SHEET 4 A 5 ASN A 169 ASP A 176 -1 N TYR A 170 O ILE A 187 SHEET 5 A 5 VAL A 274 TYR A 281 -1 O ASP A 275 N ASN A 175 SHEET 1 B 5 GLU B 12 ASP B 16 0 SHEET 2 B 5 LEU B 2 THR B 7 -1 N ILE B 3 O ILE B 15 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 SITE 1 AC1 3 LEU A 87 HOH A 530 HOH A 574 CRYST1 40.730 56.090 67.550 90.00 104.13 90.00 P 1 21 1 2 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 0.024552 0.000000 0.006181 0.00000 SCALE2 0.000000 0.017828 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015266 0.00000