HEADER LIGASE 29-APR-09 3H8K TITLE CRYSTAL STRUCTURE OF UBE2G2 COMPLXED WITH THE G2BR DOMAIN OF GP78 AT TITLE 2 1.8-A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 G2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBIQUITIN-PROTEIN LIGASE G2, UBIQUITIN CARRIER PROTEIN G2; COMPND 5 EC: 6.3.2.19; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: AUTOCRINE MOTILITY FACTOR RECEPTOR, ISOFORM 2; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: RESIDUES 573-600; COMPND 11 SYNONYM: AMF RECEPTOR, ISOFORM 2, GP78, RING FINGER PROTEIN 45; COMPND 12 EC: 6.3.2.-; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UBE2G2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET3A; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: AMFR, RNF45; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET3A KEYWDS ALPHA BETA, ALL ALPHA, LIGASE, UBL CONJUGATION PATHWAY, ENDOPLASMIC KEYWDS 2 RETICULUM, MEMBRANE, METAL-BINDING, PHOSPHOPROTEIN, RECEPTOR, KEYWDS 3 TRANSMEMBRANE, ZINC-FINGER EXPDTA X-RAY DIFFRACTION AUTHOR R.C.KALATHUR,R.DAS,J.LI,R.A.BYRD,X.JI REVDAT 6 06-SEP-23 3H8K 1 REMARK REVDAT 5 30-AUG-23 3H8K 1 AUTHOR JRNL REVDAT 4 13-OCT-21 3H8K 1 SEQADV REVDAT 3 01-NOV-17 3H8K 1 REMARK REVDAT 2 25-APR-12 3H8K 1 AUTHOR VERSN REVDAT 1 14-JUL-09 3H8K 0 JRNL AUTH R.DAS,J.MARIANO,Y.C.TSAI,R.C.KALATHUR,Z.KOSTOVA,J.LI, JRNL AUTH 2 S.G.TARASOV,R.L.MCFEETERS,A.S.ALTIERI,X.JI,R.A.BYRD, JRNL AUTH 3 A.M.WEISSMAN JRNL TITL ALLOSTERIC ACTIVATION OF E2-RING FINGER-MEDIATED JRNL TITL 2 UBIQUITYLATION BY A STRUCTURALLY DEFINED SPECIFIC E2-BINDING JRNL TITL 3 REGION OF GP78. JRNL REF MOL.CELL V. 34 674 2009 JRNL REFN ISSN 1097-2765 JRNL PMID 19560420 JRNL DOI 10.1016/J.MOLCEL.2009.05.010 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.05 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.120 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.7 REMARK 3 NUMBER OF REFLECTIONS : 15822 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1573 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 43.0610 - 3.8760 1.00 1677 187 0.1670 0.1940 REMARK 3 2 3.8760 - 3.0770 1.00 1592 171 0.1810 0.2380 REMARK 3 3 3.0770 - 2.6880 0.99 1560 175 0.2030 0.2650 REMARK 3 4 2.6880 - 2.4420 0.98 1541 167 0.2120 0.2760 REMARK 3 5 2.4420 - 2.2670 0.97 1500 170 0.2090 0.2500 REMARK 3 6 2.2670 - 2.1340 0.96 1477 159 0.1950 0.2570 REMARK 3 7 2.1340 - 2.0270 0.93 1452 158 0.2040 0.2410 REMARK 3 8 2.0270 - 1.9390 0.87 1337 155 0.2260 0.3090 REMARK 3 9 1.9390 - 1.8640 0.75 1162 129 0.2430 0.3180 REMARK 3 10 1.8640 - 1.8000 0.62 951 102 0.2310 0.2750 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 46.28 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.60500 REMARK 3 B22 (A**2) : -4.21400 REMARK 3 B33 (A**2) : -6.39000 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 1623 REMARK 3 ANGLE : 0.921 2207 REMARK 3 CHIRALITY : 0.066 232 REMARK 3 PLANARITY : 0.005 294 REMARK 3 DIHEDRAL : 15.157 629 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3H8K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000052827. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI 220 REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16657 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.3810 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 (%) : 74.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.43700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.740 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.1 REMARK 200 STARTING MODEL: PDB ENTRY 2CYX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, 100 MM TRIS, PH 8.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 292K 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 24.46000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.82000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.07500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.82000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.46000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.07500 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 TOTAL BURIED SURFACE AREA: 1970 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 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 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 99 92.91 -175.45 REMARK 500 MET A 101 28.98 47.71 REMARK 500 TYR A 103 -61.07 -108.82 REMARK 500 GLU A 104 -179.50 -178.38 REMARK 500 SER A 105 96.84 -66.23 REMARK 500 ALA A 107 150.78 -47.90 REMARK 500 PRO A 130 90.90 -43.72 REMARK 500 ASP A 132 90.43 -68.65 REMARK 500 ASP A 132 89.38 -67.74 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3FSH RELATED DB: PDB REMARK 900 THE SAME COMPLEX AT 2.76-A RESOLUTION REMARK 900 RELATED ID: 2CYX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF UBE2G2. DBREF 3H8K A 2 165 UNP P60604 UB2G2_HUMAN 2 165 DBREF 3H8K B 573 600 UNP Q9UKV5 AMFR2_HUMAN 573 600 SEQADV 3H8K TRP B 573 UNP Q9UKV5 LYS 573 ENGINEERED MUTATION SEQRES 1 A 164 ALA GLY THR ALA LEU LYS ARG LEU MET ALA GLU TYR LYS SEQRES 2 A 164 GLN LEU THR LEU ASN PRO PRO GLU GLY ILE VAL ALA GLY SEQRES 3 A 164 PRO MET ASN GLU GLU ASN PHE PHE GLU TRP GLU ALA LEU SEQRES 4 A 164 ILE MET GLY PRO GLU ASP THR CYS PHE GLU PHE GLY VAL SEQRES 5 A 164 PHE PRO ALA ILE LEU SER PHE PRO LEU ASP TYR PRO LEU SEQRES 6 A 164 SER PRO PRO LYS MET ARG PHE THR CYS GLU MET PHE HIS SEQRES 7 A 164 PRO ASN ILE TYR PRO ASP GLY ARG VAL CYS ILE SER ILE SEQRES 8 A 164 LEU HIS ALA PRO GLY ASP ASP PRO MET GLY TYR GLU SER SEQRES 9 A 164 SER ALA GLU ARG TRP SER PRO VAL GLN SER VAL GLU LYS SEQRES 10 A 164 ILE LEU LEU SER VAL VAL SER MET LEU ALA GLU PRO ASN SEQRES 11 A 164 ASP GLU SER GLY ALA ASN VAL ASP ALA SER LYS MET TRP SEQRES 12 A 164 ARG ASP ASP ARG GLU GLN PHE TYR LYS ILE ALA LYS GLN SEQRES 13 A 164 ILE VAL GLN LYS SER LEU GLY LEU SEQRES 1 B 28 TRP SER ALA ASP GLU ARG GLN ARG MET LEU VAL GLN ARG SEQRES 2 B 28 LYS ASP GLU LEU LEU GLN GLN ALA ARG LYS ARG PHE LEU SEQRES 3 B 28 ASN LYS FORMUL 3 HOH *163(H2 O) HELIX 1 1 GLY A 3 ASN A 19 1 17 HELIX 2 2 ILE A 90 HIS A 94 5 5 HELIX 3 3 SER A 115 GLU A 129 1 15 HELIX 4 4 ASN A 137 ASP A 147 1 11 HELIX 5 5 ASP A 147 GLY A 164 1 18 HELIX 6 6 SER B 574 LYS B 600 1 27 SHEET 1 A 4 ILE A 24 PRO A 28 0 SHEET 2 A 4 GLU A 36 MET A 42 -1 O LEU A 40 N VAL A 25 SHEET 3 A 4 VAL A 53 SER A 59 -1 O LEU A 58 N TRP A 37 SHEET 4 A 4 LYS A 70 PHE A 73 -1 O ARG A 72 N ILE A 57 CISPEP 1 TYR A 64 PRO A 65 0 8.29 CRYST1 48.920 60.150 61.640 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 0.020443 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016625 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016224 0.00000