HEADER PROTEIN BINDING 19-AUG-12 4GOC TITLE CRYSTAL STRUCTURE OF THE GET5 UBIQUITIN-LIKE DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: GOLGI TO ER TRAFFIC PROTEIN 5; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: UBIQUITIN-LIKE PROTEIN MDY2, MATING-DEFICIENT PROTEIN 2, COMPND 5 TRANSLATION MACHINERY-ASSOCIATED PROTEIN 24; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: GET5, MDY2, TMA24, YOL111C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: NICO(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET33B KEYWDS UBIQUITIN-LIKE DOMAIN, PROTEIN-PROTEIN INTERACTION, SGT2, PROTEIN KEYWDS 2 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.W.CHARTRON,D.G.VANDERVELDE,W.M.CLEMONS JR. REVDAT 5 28-FEB-24 4GOC 1 SEQADV REVDAT 4 16-JAN-13 4GOC 1 JRNL REVDAT 3 02-JAN-13 4GOC 1 JRNL REVDAT 2 28-NOV-12 4GOC 1 JRNL REVDAT 1 21-NOV-12 4GOC 0 JRNL AUTH J.W.CHARTRON,D.G.VANDERVELDE,W.M.CLEMONS JRNL TITL STRUCTURES OF THE SGT2/SGTA DIMERIZATION DOMAIN WITH THE JRNL TITL 2 GET5/UBL4A UBL DOMAIN REVEAL AN INTERACTION THAT FORMS A JRNL TITL 3 CONSERVED DYNAMIC INTERFACE. JRNL REF CELL REP V. 2 1620 2012 JRNL REFN ESSN 2211-1247 JRNL PMID 23142665 JRNL DOI 10.1016/J.CELREP.2012.10.010 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1066) 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.030 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 9084 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.980 REMARK 3 FREE R VALUE TEST SET COUNT : 907 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 29.0710 - 4.3572 0.97 1431 159 0.1571 0.1929 REMARK 3 2 4.3572 - 3.4602 0.98 1372 151 0.1286 0.1797 REMARK 3 3 3.4602 - 3.0234 0.99 1357 151 0.1704 0.3106 REMARK 3 4 3.0234 - 2.7472 0.99 1337 148 0.2152 0.3053 REMARK 3 5 2.7472 - 2.5504 0.98 1340 149 0.2374 0.2998 REMARK 3 6 2.5504 - 2.4001 0.99 1340 149 0.2481 0.3505 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.390 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.007 1833 REMARK 3 ANGLE : 1.103 2475 REMARK 3 CHIRALITY : 0.070 312 REMARK 3 PLANARITY : 0.005 300 REMARK 3 DIHEDRAL : 15.186 693 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 4GOC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000074435. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 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 : LIQUID NITROGEN-COOLED DOUBLE REMARK 200 CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9092 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 29.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.13300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.61300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4 M SODIUM MALONATE, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 24.68000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.79000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.81000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.79000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.68000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.81000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 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 HOH B 218 O HOH B 223 1.80 REMARK 500 OE2 GLU C 89 O HOH C 211 1.93 REMARK 500 O HOH A 219 O HOH B 214 1.98 REMARK 500 OD2 ASP B 134 O HOH B 213 2.02 REMARK 500 O HOH C 221 O HOH C 228 2.03 REMARK 500 O HOH B 232 O HOH B 237 2.03 REMARK 500 OG1 THR C 77 O HOH C 227 2.06 REMARK 500 O ASN A 129 O HOH A 208 2.06 REMARK 500 O HOH A 226 O HOH A 228 2.07 REMARK 500 O THR C 143 O HOH C 213 2.12 REMARK 500 NZ LYS A 122 O HOH A 201 2.13 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 LYS B 136 63.06 67.48 REMARK 500 ASN B 141 66.21 -115.38 REMARK 500 ASN C 129 45.27 -88.95 REMARK 500 ASN C 141 85.91 -151.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GOD RELATED DB: PDB REMARK 900 RELATED ID: 4GOE RELATED DB: PDB REMARK 900 RELATED ID: 4GOF RELATED DB: PDB DBREF 4GOC A 74 148 UNP Q12285 MDY2_YEAST 74 148 DBREF 4GOC B 74 148 UNP Q12285 MDY2_YEAST 74 148 DBREF 4GOC C 74 148 UNP Q12285 MDY2_YEAST 74 148 SEQADV 4GOC SER A 73 UNP Q12285 EXPRESSION TAG SEQADV 4GOC SER B 73 UNP Q12285 EXPRESSION TAG SEQADV 4GOC SER C 73 UNP Q12285 EXPRESSION TAG SEQRES 1 A 76 SER VAL HIS LEU THR LEU LYS LYS ILE GLN ALA PRO LYS SEQRES 2 A 76 PHE SER ILE GLU HIS ASP PHE SER PRO SER ASP THR ILE SEQRES 3 A 76 LEU GLN ILE LYS GLN HIS LEU ILE SER GLU GLU LYS ALA SEQRES 4 A 76 SER HIS ILE SER GLU ILE LYS LEU LEU LEU LYS GLY LYS SEQRES 5 A 76 VAL LEU HIS ASP ASN LEU PHE LEU SER ASP LEU LYS VAL SEQRES 6 A 76 THR PRO ALA ASN SER THR ILE THR VAL MET ILE SEQRES 1 B 76 SER VAL HIS LEU THR LEU LYS LYS ILE GLN ALA PRO LYS SEQRES 2 B 76 PHE SER ILE GLU HIS ASP PHE SER PRO SER ASP THR ILE SEQRES 3 B 76 LEU GLN ILE LYS GLN HIS LEU ILE SER GLU GLU LYS ALA SEQRES 4 B 76 SER HIS ILE SER GLU ILE LYS LEU LEU LEU LYS GLY LYS SEQRES 5 B 76 VAL LEU HIS ASP ASN LEU PHE LEU SER ASP LEU LYS VAL SEQRES 6 B 76 THR PRO ALA ASN SER THR ILE THR VAL MET ILE SEQRES 1 C 76 SER VAL HIS LEU THR LEU LYS LYS ILE GLN ALA PRO LYS SEQRES 2 C 76 PHE SER ILE GLU HIS ASP PHE SER PRO SER ASP THR ILE SEQRES 3 C 76 LEU GLN ILE LYS GLN HIS LEU ILE SER GLU GLU LYS ALA SEQRES 4 C 76 SER HIS ILE SER GLU ILE LYS LEU LEU LEU LYS GLY LYS SEQRES 5 C 76 VAL LEU HIS ASP ASN LEU PHE LEU SER ASP LEU LYS VAL SEQRES 6 C 76 THR PRO ALA ASN SER THR ILE THR VAL MET ILE FORMUL 4 HOH *104(H2 O) HELIX 1 1 THR A 97 GLU A 108 1 12 HELIX 2 2 HIS A 113 ILE A 117 5 5 HELIX 3 3 PHE A 131 LEU A 135 5 5 HELIX 4 4 THR B 97 GLU B 108 1 12 HELIX 5 5 HIS B 113 ILE B 117 5 5 HELIX 6 6 PHE B 131 LEU B 135 5 5 HELIX 7 7 THR C 97 GLU C 108 1 12 HELIX 8 8 HIS C 113 ILE C 117 5 5 HELIX 9 9 PHE C 131 LYS C 136 5 6 SHEET 1 A 5 PHE A 86 PHE A 92 0 SHEET 2 A 5 VAL A 74 LYS A 80 -1 N LEU A 78 O ILE A 88 SHEET 3 A 5 THR A 143 MET A 147 1 O ILE A 144 N THR A 77 SHEET 4 A 5 LYS A 118 LEU A 121 -1 N LEU A 120 O THR A 145 SHEET 5 A 5 LYS A 124 VAL A 125 -1 O LYS A 124 N LEU A 121 SHEET 1 B 5 PHE B 86 PHE B 92 0 SHEET 2 B 5 VAL B 74 LYS B 80 -1 N LEU B 78 O ILE B 88 SHEET 3 B 5 THR B 143 MET B 147 1 O ILE B 144 N THR B 77 SHEET 4 B 5 LYS B 118 LEU B 121 -1 N LEU B 120 O THR B 145 SHEET 5 B 5 LYS B 124 VAL B 125 -1 O LYS B 124 N LEU B 121 SHEET 1 C 5 PHE C 86 PHE C 92 0 SHEET 2 C 5 VAL C 74 LYS C 80 -1 N VAL C 74 O PHE C 92 SHEET 3 C 5 THR C 143 MET C 147 1 O ILE C 144 N THR C 77 SHEET 4 C 5 LYS C 118 LEU C 121 -1 N LYS C 118 O MET C 147 SHEET 5 C 5 LYS C 124 VAL C 125 -1 O LYS C 124 N LEU C 121 CISPEP 1 ALA A 83 PRO A 84 0 -3.31 CISPEP 2 ALA B 83 PRO B 84 0 2.44 CISPEP 3 ALA C 83 PRO C 84 0 -3.74 CRYST1 49.360 63.620 71.580 90.00 90.00 90.00 P 21 21 21 12 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 0.020259 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015718 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013970 0.00000