PDB Short entry for 2BKR HEADER PROTEIN-BINDING/HYDROLASE 18-FEB-05 2BKR TITLE NEDD8 NEDP1 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: SENTRIN-SPECIFIC PROTEASE 8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NEDP1, SENTRIN/SUMO-SPECIFIC PROTEASE SENP8, CYSTEINE COMPND 5 PROTEASE FKSG8, PROTEASE, CYSTEINE 2; COMPND 6 EC: 3.4.22.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: NEDDYLIN; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: NEDD8, UBIQUITIN-LIKE PROTEIN NEDD8; COMPND 12 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_VECTOR: PET KEYWDS PROTEIN-BINDING-HYDROLASE COMPLEX, UBIQUITIN, HYDROLASE, PROTEASE, KEYWDS 2 THIOL PROTEASE, UBL CONJUGATION PATHWAY, UBIQUITIN/HYDROLASE KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.N.SHEN,H.LIU,C.DONG,D.XIRODIMAS,J.H.NAISMITH,R.T.HAY REVDAT 4 13-JUL-11 2BKR 1 VERSN REVDAT 3 24-FEB-09 2BKR 1 VERSN REVDAT 2 17-NOV-05 2BKR 1 SOURCE REMARK REVDAT 1 15-SEP-05 2BKR 0 JRNL AUTH L.N.SHEN,H.LIU,C.DONG,D.XIRODIMAS,J.H.NAISMITH,R.T.HAY JRNL TITL STRUCTURAL BASIS OF NEDD8 UBIQUITIN DISCRIMINATION BY THE JRNL TITL 2 DENEDDYLATING ENZYME NEDP1 JRNL REF EMBO J. V. 24 1341 2005 JRNL REFN ISSN 0261-4189 JRNL PMID 15775960 JRNL DOI 10.1038/SJ.EMBOJ.7600628 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.23 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 24174 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) : 0.171 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1307 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1423 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2000 REMARK 3 BIN FREE R VALUE SET COUNT : 76 REMARK 3 BIN FREE R VALUE : 0.2410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2250 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 214 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.37000 REMARK 3 B22 (A**2) : 1.18000 REMARK 3 B33 (A**2) : -0.81000 REMARK 3 B12 (A**2) : 0.00000 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): 0.137 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.130 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.092 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.177 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2297 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3113 ; 1.569 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 286 ; 5.679 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 106 ;36.274 ;25.094 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 389 ;14.120 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;21.851 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 350 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1741 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1053 ; 0.203 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1603 ; 0.311 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 184 ; 0.196 ; 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): 33 ; 0.218 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 16 ; 0.309 ; 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): 1477 ; 1.099 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2316 ; 1.616 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 927 ; 3.018 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 797 ; 4.439 ; 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 211 REMARK 3 ORIGIN FOR THE GROUP (A): 26.0310 5.2140 23.5150 REMARK 3 T TENSOR REMARK 3 T11: -0.1043 T22: -0.1385 REMARK 3 T33: 0.0981 T12: -0.0264 REMARK 3 T13: 0.0024 T23: -0.0251 REMARK 3 L TENSOR REMARK 3 L11: 1.4071 L22: 1.9757 REMARK 3 L33: 1.3367 L12: -0.2885 REMARK 3 L13: -0.1800 L23: -0.3739 REMARK 3 S TENSOR REMARK 3 S11: -0.0058 S12: -0.0667 S13: 0.0545 REMARK 3 S21: 0.0272 S22: 0.0539 S23: -0.1012 REMARK 3 S31: -0.1042 S32: 0.0333 S33: -0.0481 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 76 REMARK 3 ORIGIN FOR THE GROUP (A): 5.7210 -2.3330 30.1930 REMARK 3 T TENSOR REMARK 3 T11: -0.1357 T22: -0.1171 REMARK 3 T33: 0.1482 T12: -0.0268 REMARK 3 T13: -0.0039 T23: 0.0279 REMARK 3 L TENSOR REMARK 3 L11: 4.9434 L22: 1.0171 REMARK 3 L33: 1.9424 L12: -0.2712 REMARK 3 L13: -1.4175 L23: 0.0739 REMARK 3 S TENSOR REMARK 3 S11: -0.1091 S12: -0.0614 S13: -0.4003 REMARK 3 S21: 0.0783 S22: 0.0086 S23: 0.1594 REMARK 3 S31: 0.0310 S32: -0.2071 S33: 0.1005 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 2BKR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-FEB-05. REMARK 100 THE PDBE ID CODE IS EBI-23030. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.008 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25411 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 54.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.45000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA):2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN BY REMARK 280 SETTING-DROP METHOD BY MIXING THE NEDP1-NEDD8 COMPLEX REMARK 280 (20MG/ML) WITH EQUAL VOLUME OF RESERVOIR SOLUTION REMARK 280 CONTAINING 20%PEG8000, 200MM NACL, 100MM PHOSPHATE CITRATE REMARK 280 PH4.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 27.31900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.79500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.11300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.79500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.31900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.11300 REMARK 290 SMTRY3 4 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 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 400 REMARK 400 COMPOUND REMARK 400 FUNCTION: POSSIBLE INVOLVEMENT IN THE RELEASE OF SENTRINS. REMARK 400 POSSIBLE ROLE DURING THE EMBRYONIC DEVELOPMENT AND REMARK 400 DIFFERENTIATION OF THE CENTRAL NERVOUS SYSTEM REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 1 CG SD CE REMARK 470 GLU A 76 CD OE1 OE2 REMARK 470 LYS A 130 CE NZ REMARK 470 ARG A 142 NE CZ NH1 NH2 REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 LYS A 146 CG CD CE REMARK 470 LYS A 153 CD CE NZ REMARK 470 GLN A 181 CD OE1 NE2 REMARK 470 GLN A 188 CD OE1 NE2 REMARK 470 LYS A 211 CD CE NZ REMARK 470 LYS A 212 CA C O CB CG CD CE NZ REMARK 470 LYS B 4 CE NZ REMARK 470 LYS B 11 CD CE NZ REMARK 470 GLU B 24 CD OE1 OE2 REMARK 470 LYS B 60 CD CE NZ 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 163 C GLY B 76 1.76 REMARK 500 N SER B 0 O HOH B 2001 2.03 REMARK 500 O HOH A 2007 O HOH A 2008 2.14 REMARK 500 O HOH A 2033 O HOH A 2083 2.17 REMARK 500 O HOH A 2121 O HOH A 2124 1.93 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 B 2024 O HOH A 2033 3645 2.18 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 79 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 162 CB - CG - OD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG B 42 NE - CZ - NH1 ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG B 42 NE - CZ - NH2 ANGL. DEV. = -9.8 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 MET A 9 -123.04 52.72 REMARK 500 SER A 42 -66.04 -124.77 REMARK 500 SER A 122 123.19 -38.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NDD RELATED DB: PDB REMARK 900 STRUCTURE OF NEDD8 REMARK 900 RELATED ID: 1R4M RELATED DB: PDB REMARK 900 APPBP1-UBA3-NEDD8, AN E1-UBIQUITIN-LIKE REMARK 900 PROTEIN COMPLEX REMARK 900 RELATED ID: 1R4N RELATED DB: PDB REMARK 900 APPBP1-UBA3-NEDD8, AN E1-UBIQUITIN-LIKE REMARK 900 PROTEIN COMPLEXWITH ATP REMARK 900 RELATED ID: 1XT9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF DEN1 IN COMPLEX WITH REMARK 900 NEDD8 REMARK 900 RELATED ID: 2BKQ RELATED DB: PDB REMARK 900 NEDD8 PROTEASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 EXTRA N-TERMINAL RESIDUE FROM CLONING SER FOR CHAIN B. REMARK 999 THE ORIGINAL SAMPLE FOR CHAIN B CONTAINS 82 RESIDUES REMARK 999 INCLUDING GLY GLY LEU ARG GLN (77-81) BUT THESE RESIDUES REMARK 999 ARE CLEAVED OFF BY THE PROTEASE DURING THE COMPLEX REMARK 999 FORMATION. THESE RESIDUES ARE NOT THEREFORE PART OF REMARK 999 OF THE CRYSTALLIZED COMPLEX. DBREF 2BKR A 1 212 UNP Q96LD8 SENP8_HUMAN 1 212 DBREF 2BKR B 0 0 PDB 2BKR 2BKR 0 0 DBREF 2BKR B 1 76 UNP Q15843 NEDD8_HUMAN 1 76 SEQADV 2BKR SER A 47 UNP Q96LD8 CYS 47 CONFLICT SEQADV 2BKR SER A 101 UNP Q96LD8 THR 101 CONFLICT SEQRES 1 A 212 MET ASP PRO VAL VAL LEU SER TYR MET ASP SER LEU LEU SEQRES 2 A 212 ARG GLN SER ASP VAL SER LEU LEU ASP PRO PRO SER TRP SEQRES 3 A 212 LEU ASN ASP HIS ILE ILE GLY PHE ALA PHE GLU TYR PHE SEQRES 4 A 212 ALA ASN SER GLN PHE HIS ASP SER SER ASP HIS VAL SER SEQRES 5 A 212 PHE ILE SER PRO GLU VAL THR GLN PHE ILE LYS CYS THR SEQRES 6 A 212 SER ASN PRO ALA GLU ILE ALA MET PHE LEU GLU PRO LEU SEQRES 7 A 212 ASP LEU PRO ASN LYS ARG VAL VAL PHE LEU ALA ILE ASN SEQRES 8 A 212 ASP ASN SER ASN GLN ALA ALA GLY GLY SER HIS TRP SER SEQRES 9 A 212 LEU LEU VAL TYR LEU GLN ASP LYS ASN SER PHE PHE HIS SEQRES 10 A 212 TYR ASP SER HIS SER ARG SER ASN SER VAL HIS ALA LYS SEQRES 11 A 212 GLN VAL ALA GLU LYS LEU GLU ALA PHE LEU GLY ARG LYS SEQRES 12 A 212 GLY ASP LYS LEU ALA PHE VAL GLU GLU LYS ALA PRO ALA SEQRES 13 A 212 GLN GLN ASN SER TYR ASP CYS GLY MET TYR VAL ILE CYS SEQRES 14 A 212 ASN THR GLU ALA LEU CYS GLN ASN PHE PHE ARG GLN GLN SEQRES 15 A 212 THR GLU SER LEU LEU GLN LEU LEU THR PRO ALA TYR ILE SEQRES 16 A 212 THR LYS LYS ARG GLY GLU TRP LYS ASP LEU ILE ALA THR SEQRES 17 A 212 LEU ALA LYS LYS SEQRES 1 B 77 SER MET LEU ILE LYS VAL LYS THR LEU THR GLY LYS GLU SEQRES 2 B 77 ILE GLU ILE ASP ILE GLU PRO THR ASP LYS VAL GLU ARG SEQRES 3 B 77 ILE LYS GLU ARG VAL GLU GLU LYS GLU GLY ILE PRO PRO SEQRES 4 B 77 GLN GLN GLN ARG LEU ILE TYR SER GLY LYS GLN MET ASN SEQRES 5 B 77 ASP GLU LYS THR ALA ALA ASP TYR LYS ILE LEU GLY GLY SEQRES 6 B 77 SER VAL LEU HIS LEU VAL LEU ALA LEU ARG GLY GLY FORMUL 3 HOH *214(H2 O) HELIX 1 1 GLN A 15 LEU A 20 1 6 HELIX 2 2 ASN A 28 SER A 42 1 15 HELIX 3 3 PHE A 44 SER A 48 5 5 HELIX 4 4 SER A 55 THR A 65 1 11 HELIX 5 5 ASN A 67 GLU A 76 1 10 HELIX 6 6 PRO A 77 LYS A 83 5 7 HELIX 7 7 ASP A 111 ASN A 113 5 3 HELIX 8 8 ASN A 125 GLY A 141 1 17 HELIX 9 9 ASP A 162 ARG A 180 1 19 HELIX 10 10 SER A 185 LEU A 190 1 6 HELIX 11 11 THR A 191 LYS A 211 1 21 HELIX 12 12 LYS B 22 GLY B 35 1 14 HELIX 13 13 PRO B 37 GLN B 39 5 3 SHEET 1 AA 2 VAL A 4 TYR A 8 0 SHEET 2 AA 2 SER A 11 ARG A 14 -1 O SER A 11 N TYR A 8 SHEET 1 AB 5 VAL A 51 ILE A 54 0 SHEET 2 AB 5 VAL A 85 ASN A 91 1 O VAL A 85 N SER A 52 SHEET 3 AB 5 TRP A 103 LEU A 109 -1 O SER A 104 N ILE A 90 SHEET 4 AB 5 SER A 114 TYR A 118 -1 O SER A 114 N LEU A 109 SHEET 5 AB 5 PHE A 149 GLU A 151 1 O VAL A 150 N HIS A 117 SHEET 1 BA 5 GLU B 12 ILE B 17 0 SHEET 2 BA 5 MET B 1 THR B 7 -1 O MET B 1 N ILE B 17 SHEET 3 BA 5 VAL B 66 LEU B 71 1 O LEU B 67 N LYS B 6 SHEET 4 BA 5 GLN B 41 TYR B 45 -1 O ARG B 42 N VAL B 70 SHEET 5 BA 5 LYS B 48 GLN B 49 -1 O LYS B 48 N TYR B 45 CISPEP 1 PRO A 23 PRO A 24 0 5.80 CRYST1 54.638 74.226 79.590 90.00 90.00 90.00 P 21 21 21 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 0.018302 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013472 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012564 0.00000