HEADER MEMBRANE PROTEIN 03-APR-03 1OXZ TITLE CRYSTAL STRUCTURE OF THE HUMAN GGA1 GAT DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYLATION FACTOR BINDING PROTEIN GGA1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GAT DOMAIN; COMPND 5 SYNONYM: GOLGI-LOCALIZED, GAMMA EAR-CONTAINING, ARF-BINDING PROTEIN COMPND 6 1, GAMMA-ADAPTIN RELATED PROTEIN 1; COMPND 7 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: GGA1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX2T KEYWDS GGA1, GAT DOMAIN, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.ZHU,P.ZHAI,X.HE,S.TERZYAN,R.ZHANG,A.JOACHIMIAK,J.TANG,X.C.ZHANG REVDAT 4 14-FEB-24 1OXZ 1 REMARK REVDAT 3 24-FEB-09 1OXZ 1 VERSN REVDAT 2 03-JUN-03 1OXZ 1 JRNL REVDAT 1 15-APR-03 1OXZ 0 JRNL AUTH G.ZHU,P.ZHAI,X.HE,S.TERZYAN,R.ZHANG,A.JOACHIMIAK,J.TANG, JRNL AUTH 2 X.C.ZHANG JRNL TITL CRYSTAL STRUCTURE OF HUMAN GGA1 GAT DOMAIN JRNL REF BIOCHEMISTRY V. 42 6392 2003 JRNL REFN ISSN 0006-2960 JRNL PMID 12767220 JRNL DOI 10.1021/BI034334N REMARK 2 REMARK 2 RESOLUTION. 2.80 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.1 REMARK 3 NUMBER OF REFLECTIONS : 6413 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) : 0.241 REMARK 3 FREE R VALUE : 0.285 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.900 REMARK 3 FREE R VALUE TEST SET COUNT : 699 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.90 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 568 REMARK 3 BIN R VALUE (WORKING SET) : 0.4540 REMARK 3 BIN FREE R VALUE : 0.5500 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 64 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.069 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1051 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 93.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.60000 REMARK 3 B22 (A**2) : 11.60000 REMARK 3 B33 (A**2) : -23.20000 REMARK 3 B12 (A**2) : 35.57000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.42 REMARK 3 ESD FROM SIGMAA (A) : 0.45 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.49 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.51 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 19.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.790 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) : 7.190 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 9.870 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 11.090; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 14.120; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.30 REMARK 3 BSOL : 30.27 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 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OXZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-APR-03. REMARK 100 THE DEPOSITION ID IS D_1000018786. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC OPTICS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6418 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.04400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 42.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.48900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD 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 (%): 63.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM SULFATE, MES, ETHYLENE GLYCOL REMARK 280 , PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 34.47500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 34.47500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 34.47500 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: 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 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 LYS A 141 REMARK 465 GLN A 142 REMARK 465 GLY A 143 REMARK 465 ILE A 144 REMARK 465 VAL A 145 REMARK 465 LYS A 146 REMARK 465 SER A 147 REMARK 465 ASP A 148 REMARK 465 PRO A 149 REMARK 465 LYS A 150 REMARK 465 LEU A 151 REMARK 465 PRO A 152 REMARK 465 ASP A 153 REMARK 465 ASP A 154 REMARK 465 THR A 155 REMARK 465 THR A 156 REMARK 465 PHE A 157 REMARK 465 PRO A 158 REMARK 465 LEU A 159 REMARK 465 PRO A 160 REMARK 465 PRO A 161 REMARK 465 PRO A 162 REMARK 465 ARG A 163 REMARK 465 PRO A 164 REMARK 465 LYS A 165 REMARK 465 ASN A 166 REMARK 465 VAL A 167 REMARK 465 ILE A 168 REMARK 465 PHE A 169 REMARK 465 GLU A 170 REMARK 465 VAL A 303 REMARK 465 ASN A 304 REMARK 465 GLY A 305 REMARK 465 ASP A 306 REMARK 465 ALA A 307 REMARK 465 THR A 308 REMARK 465 ALA A 309 REMARK 465 GLY A 310 REMARK 465 SER A 311 REMARK 465 ILE A 312 REMARK 465 PRO A 313 REMARK 465 GLY A 314 REMARK 465 SER A 315 REMARK 465 THR A 316 REMARK 465 SER A 317 REMARK 465 ALA A 318 REMARK 465 LEU A 319 REMARK 465 LEU A 320 REMARK 465 ASP A 321 REMARK 465 LEU A 322 REMARK 465 SER A 323 REMARK 465 GLY A 324 REMARK 465 LEU A 325 REMARK 465 ASP A 326 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 SER A 175 3.61 -54.93 REMARK 500 LYS A 176 -32.87 -130.00 REMARK 500 SER A 184 179.03 -53.48 REMARK 500 PRO A 187 -4.66 -53.61 REMARK 500 ARG A 207 -70.32 -52.57 REMARK 500 VAL A 232 -39.15 -38.97 REMARK 500 HIS A 235 50.44 -101.37 REMARK 500 GLN A 237 -6.44 163.59 REMARK 500 ALA A 240 102.49 50.81 REMARK 500 ALA A 241 103.65 -53.36 REMARK 500 ALA A 242 82.03 -55.28 REMARK 500 TYR A 253 -70.79 -44.77 REMARK 500 GLN A 254 -39.87 -38.82 REMARK 500 ASN A 273 85.51 -156.58 REMARK 500 ASN A 292 49.15 -100.73 REMARK 500 LEU A 293 -19.63 -156.42 REMARK 500 GLN A 296 -116.29 -80.63 REMARK 500 LEU A 297 -86.43 -22.55 REMARK 500 VAL A 298 -105.68 -46.92 REMARK 500 ARG A 299 -0.99 -43.18 REMARK 500 GLU A 301 -90.72 -72.81 REMARK 500 REMARK 500 REMARK: NULL DBREF 1OXZ A 141 326 UNP Q9UJY5 GGA1_HUMAN 141 326 SEQRES 1 A 186 LYS GLN GLY ILE VAL LYS SER ASP PRO LYS LEU PRO ASP SEQRES 2 A 186 ASP THR THR PHE PRO LEU PRO PRO PRO ARG PRO LYS ASN SEQRES 3 A 186 VAL ILE PHE GLU ASP GLU GLU LYS SER LYS MET LEU ALA SEQRES 4 A 186 ARG LEU LEU LYS SER SER HIS PRO GLU ASP LEU ARG ALA SEQRES 5 A 186 ALA ASN LYS LEU ILE LYS GLU MET VAL GLN GLU ASP GLN SEQRES 6 A 186 LYS ARG MET GLU LYS ILE SER LYS ARG VAL ASN ALA ILE SEQRES 7 A 186 GLU GLU VAL ASN ASN ASN VAL LYS LEU LEU THR GLU MET SEQRES 8 A 186 VAL MET SER HIS SER GLN GLY GLY ALA ALA ALA GLY SER SEQRES 9 A 186 SER GLU ASP LEU MET LYS GLU LEU TYR GLN ARG CYS GLU SEQRES 10 A 186 ARG MET ARG PRO THR LEU PHE ARG LEU ALA SER ASP THR SEQRES 11 A 186 GLU ASP ASN ASP GLU ALA LEU ALA GLU ILE LEU GLN ALA SEQRES 12 A 186 ASN ASP ASN LEU THR GLN VAL ILE ASN LEU TYR LYS GLN SEQRES 13 A 186 LEU VAL ARG GLY GLU GLU VAL ASN GLY ASP ALA THR ALA SEQRES 14 A 186 GLY SER ILE PRO GLY SER THR SER ALA LEU LEU ASP LEU SEQRES 15 A 186 SER GLY LEU ASP HELIX 1 1 GLU A 173 LYS A 183 1 11 HELIX 2 2 HIS A 186 HIS A 235 1 50 HELIX 3 3 SER A 245 THR A 270 1 26 HELIX 4 4 ASN A 273 LYS A 295 1 23 HELIX 5 5 GLN A 296 GLU A 301 1 6 CRYST1 83.400 83.400 68.950 90.00 90.00 120.00 P 63 6 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 0.011990 0.006923 0.000000 0.00000 SCALE2 0.000000 0.013845 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014503 0.00000