PDB Short entry for 2GRO HEADER LIGASE 24-APR-06 2GRO TITLE CRYSTAL STRUCTURE OF HUMAN RANGAP1-UBC9-N85Q COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 I; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBIQUITIN-PROTEIN LIGASE I, UBIQUITIN CARRIER PROTEIN I, COMPND 5 SUMO-1-PROTEIN LIGASE, SUMO-1-CONJUGATING ENZYME, UBIQUITIN CARRIER COMPND 6 PROTEIN 9, P18; COMPND 7 EC: 6.3.2.19; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: RAN GTPASE-ACTIVATING PROTEIN 1; COMPND 12 CHAIN: B; COMPND 13 FRAGMENT: C-TERMINAL DOMAIN (RESIDUES 419-587); COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UBE2I, UBC9, UBCE9; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21DE3 CODON PLUS RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: RANGAP1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21DE3 CODON PLUS RIL; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PSMT3 KEYWDS UBIQUITIN, CONJUGATION, SMALL UBIQUITIN LIKE MODIFER, SMT3, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR A.A.YUNUS,C.D.LIMA REVDAT 6 14-FEB-24 2GRO 1 REMARK REVDAT 5 20-OCT-21 2GRO 1 SEQADV REVDAT 4 18-OCT-17 2GRO 1 REMARK REVDAT 3 24-FEB-09 2GRO 1 VERSN REVDAT 2 20-JUN-06 2GRO 1 JRNL REVDAT 1 30-MAY-06 2GRO 0 JRNL AUTH A.A.YUNUS,C.D.LIMA JRNL TITL LYSINE ACTIVATION AND FUNCTIONAL ANALYSIS OF E2-MEDIATED JRNL TITL 2 CONJUGATION IN THE SUMO PATHWAY. JRNL REF NAT.STRUCT.MOL.BIOL. V. 13 491 2006 JRNL REFN ISSN 1545-9993 JRNL PMID 16732283 JRNL DOI 10.1038/NSMB1104 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 687535.938 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 39163 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 SET) : 0.185 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1929 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3446 REMARK 3 BIN R VALUE (WORKING SET) : 0.2140 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 174 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2473 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 428 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.29000 REMARK 3 B22 (A**2) : 0.47000 REMARK 3 B33 (A**2) : -0.76000 REMARK 3 B12 (A**2) : -1.69000 REMARK 3 B13 (A**2) : -1.55000 REMARK 3 B23 (A**2) : 1.90000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.11 REMARK 3 LOW RESOLUTION CUTOFF (A) : 6.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.15 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.930 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.140 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.780 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.230 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.170 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.42 REMARK 3 BSOL : 57.74 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2GRO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000037472. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : MONOCHROMATOR KOHZU HLD-4 DOUBLE REMARK 200 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39181 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.14700 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M LITHIUM SULFATE, 0.5M AMMONIUM REMARK 280 SULFATE, 50MM SODIUM CITRATE, PH 5.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 SER A 158 REMARK 465 SER B 418 REMARK 465 THR B 419 REMARK 465 GLY B 420 REMARK 465 GLU B 421 REMARK 465 PRO B 422 REMARK 465 ALA B 423 REMARK 465 PRO B 424 REMARK 465 VAL B 425 REMARK 465 LEU B 426 REMARK 465 SER B 427 REMARK 465 SER B 428 REMARK 465 PRO B 429 REMARK 465 PRO B 430 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 HIS A 83 138.02 -171.70 REMARK 500 LYS A 101 -107.02 -115.22 REMARK 500 ASN A 140 86.90 -155.21 REMARK 500 ASN B 567 125.80 -172.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GRN RELATED DB: PDB REMARK 900 RELATED ID: 2GRP RELATED DB: PDB REMARK 900 RELATED ID: 2GRQ RELATED DB: PDB REMARK 900 RELATED ID: 2GRR RELATED DB: PDB DBREF 2GRO A 1 158 UNP P63279 UBE2I_HUMAN 1 158 DBREF 2GRO B 419 587 UNP P46060 RGP1_HUMAN 419 587 SEQADV 2GRO GLY A -2 UNP P63279 CLONING ARTIFACT SEQADV 2GRO SER A -1 UNP P63279 CLONING ARTIFACT SEQADV 2GRO HIS A 0 UNP P63279 CLONING ARTIFACT SEQADV 2GRO GLN A 85 UNP P63279 ASN 85 ENGINEERED MUTATION SEQADV 2GRO SER B 418 UNP P46060 CLONING ARTIFACT SEQRES 1 A 161 GLY SER HIS MET SER GLY ILE ALA LEU SER ARG LEU ALA SEQRES 2 A 161 GLN GLU ARG LYS ALA TRP ARG LYS ASP HIS PRO PHE GLY SEQRES 3 A 161 PHE VAL ALA VAL PRO THR LYS ASN PRO ASP GLY THR MET SEQRES 4 A 161 ASN LEU MET ASN TRP GLU CYS ALA ILE PRO GLY LYS LYS SEQRES 5 A 161 GLY THR PRO TRP GLU GLY GLY LEU PHE LYS LEU ARG MET SEQRES 6 A 161 LEU PHE LYS ASP ASP TYR PRO SER SER PRO PRO LYS CYS SEQRES 7 A 161 LYS PHE GLU PRO PRO LEU PHE HIS PRO GLN VAL TYR PRO SEQRES 8 A 161 SER GLY THR VAL CYS LEU SER ILE LEU GLU GLU ASP LYS SEQRES 9 A 161 ASP TRP ARG PRO ALA ILE THR ILE LYS GLN ILE LEU LEU SEQRES 10 A 161 GLY ILE GLN GLU LEU LEU ASN GLU PRO ASN ILE GLN ASP SEQRES 11 A 161 PRO ALA GLN ALA GLU ALA TYR THR ILE TYR CYS GLN ASN SEQRES 12 A 161 ARG VAL GLU TYR GLU LYS ARG VAL ARG ALA GLN ALA LYS SEQRES 13 A 161 LYS PHE ALA PRO SER SEQRES 1 B 170 SER THR GLY GLU PRO ALA PRO VAL LEU SER SER PRO PRO SEQRES 2 B 170 PRO ALA ASP VAL SER THR PHE LEU ALA PHE PRO SER PRO SEQRES 3 B 170 GLU LYS LEU LEU ARG LEU GLY PRO LYS SER SER VAL LEU SEQRES 4 B 170 ILE ALA GLN GLN THR ASP THR SER ASP PRO GLU LYS VAL SEQRES 5 B 170 VAL SER ALA PHE LEU LYS VAL SER SER VAL PHE LYS ASP SEQRES 6 B 170 GLU ALA THR VAL ARG MET ALA VAL GLN ASP ALA VAL ASP SEQRES 7 B 170 ALA LEU MET GLN LYS ALA PHE ASN SER SER SER PHE ASN SEQRES 8 B 170 SER ASN THR PHE LEU THR ARG LEU LEU VAL HIS MET GLY SEQRES 9 B 170 LEU LEU LYS SER GLU ASP LYS VAL LYS ALA ILE ALA ASN SEQRES 10 B 170 LEU TYR GLY PRO LEU MET ALA LEU ASN HIS MET VAL GLN SEQRES 11 B 170 GLN ASP TYR PHE PRO LYS ALA LEU ALA PRO LEU LEU LEU SEQRES 12 B 170 ALA PHE VAL THR LYS PRO ASN SER ALA LEU GLU SER CYS SEQRES 13 B 170 SER PHE ALA ARG HIS SER LEU LEU GLN THR LEU TYR LYS SEQRES 14 B 170 VAL FORMUL 3 HOH *428(H2 O) HELIX 1 1 SER A 2 ASP A 19 1 18 HELIX 2 2 LEU A 94 GLU A 98 5 5 HELIX 3 3 THR A 108 GLU A 122 1 15 HELIX 4 4 GLN A 130 ASN A 140 1 11 HELIX 5 5 ASN A 140 PHE A 155 1 16 HELIX 6 6 ASP B 433 PHE B 440 1 8 HELIX 7 7 SER B 442 ARG B 448 1 7 HELIX 8 8 LYS B 452 GLN B 460 1 9 HELIX 9 9 ASP B 465 SER B 478 1 14 HELIX 10 10 GLU B 483 ASN B 503 1 21 HELIX 11 11 ASN B 508 MET B 520 1 13 HELIX 12 12 LEU B 535 VAL B 546 1 12 HELIX 13 13 PRO B 552 ALA B 554 5 3 HELIX 14 14 LEU B 555 LYS B 565 1 11 HELIX 15 15 ASN B 567 SER B 572 1 6 HELIX 16 16 CYS B 573 VAL B 587 1 15 SHEET 1 A 4 VAL A 25 LYS A 30 0 SHEET 2 A 4 MET A 36 PRO A 46 -1 O ASN A 37 N THR A 29 SHEET 3 A 4 LEU A 57 LEU A 63 -1 O LEU A 60 N CYS A 43 SHEET 4 A 4 LYS A 74 PHE A 77 -1 O LYS A 74 N LEU A 63 CISPEP 1 TYR A 68 PRO A 69 0 0.49 CISPEP 2 GLU A 78 PRO A 79 0 0.87 CRYST1 39.295 44.785 61.027 72.58 72.06 75.45 P 1 1 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 0.025450 -0.006600 -0.006850 0.00000 SCALE2 0.000000 0.023070 -0.005730 0.00000 SCALE3 0.000000 0.000000 0.017750 0.00000