HEADER PROTEIN BINDING 08-JAN-12 3VEJ TITLE CRYSTAL STRUCTURE OF THE GET5 CARBOXYL DOMAIN FROM S. CEREVISIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-LIKE PROTEIN MDY2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CARBOXYL DOMAIN RESIDUES 175-212; COMPND 5 SYNONYM: GOLGI TO ER TRAFFIC PROTEIN 5, MATING-DEFICIENT PROTEIN 2, COMPND 6 TRANSLATION MACHINERY-ASSOCIATED PROTEIN 24; COMPND 7 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: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)STAR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET-33B KEYWDS ALPHA HELICAL, DIMERIZATION, HOMODIMERIZATION, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.W.CHARTRON,D.G.VANDERVELDE,M.RAO,W.M.CLEMONS JR. REVDAT 3 28-FEB-24 3VEJ 1 REMARK SEQADV REVDAT 2 28-MAR-12 3VEJ 1 JRNL REVDAT 1 25-JAN-12 3VEJ 0 JRNL AUTH J.W.CHARTRON,D.G.VANDERVELDE,M.RAO,W.M.CLEMONS JRNL TITL GET5 CARBOXYL-TERMINAL DOMAIN IS A NOVEL DIMERIZATION MOTIF JRNL TITL 2 THAT TETHERS AN EXTENDED GET4/GET5 COMPLEX. JRNL REF J.BIOL.CHEM. V. 287 8310 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22262836 JRNL DOI 10.1074/JBC.M111.333252 REMARK 2 REMARK 2 RESOLUTION. 1.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 1.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 18274 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1089 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 24.8438 - 2.4592 0.97 2176 135 0.1714 0.1870 REMARK 3 2 2.4592 - 1.9522 0.98 2155 134 0.1656 0.2108 REMARK 3 3 1.9522 - 1.7055 0.98 2140 154 0.1611 0.1714 REMARK 3 4 1.7055 - 1.5496 0.98 2114 153 0.1480 0.2000 REMARK 3 5 1.5496 - 1.4385 0.99 2202 135 0.1649 0.1914 REMARK 3 6 1.4385 - 1.3537 0.98 2153 116 0.1984 0.2431 REMARK 3 7 1.3537 - 1.2859 0.99 2161 121 0.2519 0.2723 REMARK 3 8 1.2859 - 1.2299 0.96 2084 141 0.3097 0.3587 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 37.41 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.91 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.40350 REMARK 3 B22 (A**2) : -1.17700 REMARK 3 B33 (A**2) : 1.58040 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.84570 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 : 0.010 740 REMARK 3 ANGLE : 1.082 1020 REMARK 3 CHIRALITY : 0.078 112 REMARK 3 PLANARITY : 0.007 136 REMARK 3 DIHEDRAL : 13.637 288 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 3VEJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000069945. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 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) : 1.000 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 : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18288 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.230 REMARK 200 RESOLUTION RANGE LOW (A) : 46.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.6300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.87 REMARK 200 R MERGE FOR SHELL (I) : 0.60900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.050 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 28.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.4 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 CITRATE, PH 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K 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 23.17000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS THE DIMER IN THE ASYMMETRIC UNIT. 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: 1890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 SER A 172 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 LYS B 212 CB CG 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 OE1 GLU A 202 O HOH A 341 2.15 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 OD1 ASP B 174 O HOH A 336 1655 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2LNZ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE S. CEREVISIAE HOMOLOG REMARK 900 RELATED ID: 2LO0 RELATED DB: PDB DBREF 3VEJ A 175 212 UNP Q12285 MDY2_YEAST 175 212 DBREF 3VEJ B 175 212 UNP Q12285 MDY2_YEAST 175 212 SEQADV 3VEJ SER A 172 UNP Q12285 EXPRESSION TAG SEQADV 3VEJ VAL A 173 UNP Q12285 EXPRESSION TAG SEQADV 3VEJ ASP A 174 UNP Q12285 EXPRESSION TAG SEQADV 3VEJ SER B 172 UNP Q12285 EXPRESSION TAG SEQADV 3VEJ VAL B 173 UNP Q12285 EXPRESSION TAG SEQADV 3VEJ ASP B 174 UNP Q12285 EXPRESSION TAG SEQRES 1 A 41 SER VAL ASP LEU THR VAL PRO TRP ASP ASP ILE GLU ALA SEQRES 2 A 41 LEU LEU LYS ASN ASN PHE GLU ASN ASP GLN ALA ALA VAL SEQRES 3 A 41 ARG GLN VAL MET GLU ARG LEU GLN LYS GLY TRP SER LEU SEQRES 4 A 41 ALA LYS SEQRES 1 B 41 SER VAL ASP LEU THR VAL PRO TRP ASP ASP ILE GLU ALA SEQRES 2 B 41 LEU LEU LYS ASN ASN PHE GLU ASN ASP GLN ALA ALA VAL SEQRES 3 B 41 ARG GLN VAL MET GLU ARG LEU GLN LYS GLY TRP SER LEU SEQRES 4 B 41 ALA LYS HET PO4 B 301 5 HETNAM PO4 PHOSPHATE ION FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *86(H2 O) HELIX 1 1 PRO A 178 PHE A 190 1 13 HELIX 2 2 ASP A 193 ALA A 211 1 19 HELIX 3 3 PRO B 178 PHE B 190 1 13 HELIX 4 4 ASP B 193 ALA B 211 1 19 SITE 1 AC1 6 ARG A 203 HOH A 331 ARG B 203 LYS B 212 SITE 2 AC1 6 HOH B 433 HOH B 434 CRYST1 25.020 46.340 28.270 90.00 96.90 90.00 P 1 21 1 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 0.039968 0.000000 0.004837 0.00000 SCALE2 0.000000 0.021580 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035631 0.00000