PDB Short entry for 4ILE HEADER TRANSPORT PROTEIN 31-DEC-12 4ILE TITLE STRUCTURE OF HUMAN ADP-RIBOSYLATION FACTOR-LIKE 8A BINDING TO GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 8A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-181; COMPND 5 SYNONYM: ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 10B, NOVEL SMALL G COMPND 6 PROTEIN INDISPENSABLE FOR EQUAL CHROMOSOME SEGREGATION 2; 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: ARL8A, ARL10B, GIE2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-2 KEYWDS GTPASE, MEMBRANE TRAFFICKING, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.XIE,J.REN,Z.CHENG,H.QIAN REVDAT 1 01-JAN-14 4ILE 0 JRNL AUTH Y.XIE,J.REN,Z.CHENG,H.QIAN JRNL TITL STRUCTURE OF HUMAN ADP-RIBOSYLATION FACTOR-LIKE 8A BINDING JRNL TITL 2 TO GDP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 5242 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.540 REMARK 3 FREE R VALUE TEST SET COUNT : 238 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 39.3192 - 3.3711 1.00 2600 120 0.1700 0.2369 REMARK 3 2 3.3711 - 2.6759 0.98 2404 118 0.2005 0.3279 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 : 0.31 REMARK 3 B_SOL : 7.85 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.560 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.78 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.47060 REMARK 3 B22 (A**2) : -2.53700 REMARK 3 B33 (A**2) : -0.93370 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 : 0.009 1477 REMARK 3 ANGLE : 1.285 1997 REMARK 3 CHIRALITY : 0.086 220 REMARK 3 PLANARITY : 0.004 248 REMARK 3 DIHEDRAL : 18.171 561 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 4ILE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JAN-13. REMARK 100 THE RCSB ID CODE IS RCSB076898. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9724 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5242 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.676 REMARK 200 RESOLUTION RANGE LOW (A) : 39.315 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.30300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.980 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: 2H18 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 4000, 200MM NACL, 100MM TRIS- REMARK 280 HCL (PH7.4), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 59.01600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.68700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 59.01600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.68700 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLY A -1 REMARK 465 SER A 0 REMARK 465 MSE A 1 REMARK 465 ILE A 2 REMARK 465 ALA A 3 REMARK 465 LEU A 4 REMARK 465 PHE A 5 REMARK 465 ASN A 6 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 GLU A 47 O HOH A 303 2.16 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 GDP A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2H18 RELATED DB: PDB REMARK 900 SAME PROTEIN, THE MONOCLINIC SPACE GROUP P21 WITH UNIT-CELL REMARK 900 PARAMETERS A = 39.41, B = 66.46, C = 39.65, BETA = 117.54 REMARK 900 (DEGREE). DBREF 4ILE A 1 181 UNP Q96BM9 ARL8A_HUMAN 1 181 SEQADV 4ILE GLY A -1 UNP Q96BM9 EXPRESSION TAG SEQADV 4ILE SER A 0 UNP Q96BM9 EXPRESSION TAG SEQADV 4ILE ARG A 182 UNP Q96BM9 EXPRESSION TAG SEQRES 1 A 184 GLY SER MSE ILE ALA LEU PHE ASN LYS LEU LEU ASP TRP SEQRES 2 A 184 PHE LYS ALA LEU PHE TRP LYS GLU GLU MSE GLU LEU THR SEQRES 3 A 184 LEU VAL GLY LEU GLN TYR SER GLY LYS THR THR PHE VAL SEQRES 4 A 184 ASN VAL ILE ALA SER GLY GLN PHE ASN GLU ASP MSE ILE SEQRES 5 A 184 PRO THR VAL GLY PHE ASN MSE ARG LYS ILE THR LYS GLY SEQRES 6 A 184 ASN VAL THR ILE LYS LEU TRP ASP ILE GLY GLY GLN PRO SEQRES 7 A 184 ARG PHE ARG SER MSE TRP GLU ARG TYR CYS ARG GLY VAL SEQRES 8 A 184 SER ALA ILE VAL TYR MSE VAL ASP ALA ALA ASP GLN GLU SEQRES 9 A 184 LYS ILE GLU ALA SER LYS ASN GLU LEU HIS ASN LEU LEU SEQRES 10 A 184 ASP LYS PRO GLN LEU GLN GLY ILE PRO VAL LEU VAL LEU SEQRES 11 A 184 GLY ASN LYS ARG ASP LEU PRO GLY ALA LEU ASP GLU LYS SEQRES 12 A 184 GLU LEU ILE GLU LYS MSE ASN LEU SER ALA ILE GLN ASP SEQRES 13 A 184 ARG GLU ILE CYS CYS TYR SER ILE SER CYS LYS GLU LYS SEQRES 14 A 184 ASP ASN ILE ASP ILE THR LEU GLN TRP LEU ILE GLN HIS SEQRES 15 A 184 SER ARG MODRES 4ILE MSE A 21 MET SELENOMETHIONINE MODRES 4ILE MSE A 49 MET SELENOMETHIONINE MODRES 4ILE MSE A 57 MET SELENOMETHIONINE MODRES 4ILE MSE A 81 MET SELENOMETHIONINE MODRES 4ILE MSE A 95 MET SELENOMETHIONINE MODRES 4ILE MSE A 147 MET SELENOMETHIONINE HET MSE A 21 8 HET MSE A 49 8 HET MSE A 57 8 HET MSE A 81 8 HET MSE A 95 8 HET MSE A 147 8 HET GDP A 201 28 HETNAM MSE SELENOMETHIONINE HETNAM GDP GUANOSINE-5'-DIPHOSPHATE FORMUL 1 MSE 6(C5 H11 N O2 SE) FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 HOH *55(H2 O) HELIX 1 1 LEU A 8 LYS A 18 1 11 HELIX 2 2 GLY A 32 ALA A 41 1 10 HELIX 3 3 GLN A 75 ARG A 77 5 3 HELIX 4 4 PHE A 78 CYS A 86 1 9 HELIX 5 5 ASP A 100 GLU A 102 5 3 HELIX 6 6 LYS A 103 LEU A 115 1 13 HELIX 7 7 ASP A 116 GLN A 121 5 6 HELIX 8 8 ASP A 139 MSE A 147 1 9 HELIX 9 9 ASN A 148 ILE A 152 5 5 HELIX 10 10 ASN A 169 GLN A 179 1 11 SHEET 1 A 7 ASN A 46 MSE A 49 0 SHEET 2 A 7 ARG A 58 LYS A 62 -1 O THR A 61 N ASN A 46 SHEET 3 A 7 VAL A 65 ASP A 71 -1 O ILE A 67 N ILE A 60 SHEET 4 A 7 GLU A 22 GLY A 27 1 N LEU A 23 O LYS A 68 SHEET 5 A 7 ILE A 92 ASP A 97 1 O VAL A 93 N THR A 24 SHEET 6 A 7 VAL A 125 ASN A 130 1 O LEU A 126 N ILE A 92 SHEET 7 A 7 ILE A 157 SER A 161 1 O CYS A 158 N VAL A 127 LINK C GLU A 20 N MSE A 21 1555 1555 1.33 LINK C MSE A 21 N GLU A 22 1555 1555 1.33 LINK C ASP A 48 N MSE A 49 1555 1555 1.33 LINK C MSE A 49 N ILE A 50 1555 1555 1.33 LINK C ASN A 56 N MSE A 57 1555 1555 1.33 LINK C MSE A 57 N ARG A 58 1555 1555 1.33 LINK C SER A 80 N MSE A 81 1555 1555 1.33 LINK C MSE A 81 N TRP A 82 1555 1555 1.33 LINK C TYR A 94 N MSE A 95 1555 1555 1.32 LINK C MSE A 95 N VAL A 96 1555 1555 1.33 LINK C LYS A 146 N MSE A 147 1555 1555 1.33 LINK C MSE A 147 N ASN A 148 1555 1555 1.33 CISPEP 1 ILE A 50 PRO A 51 0 4.04 SITE 1 AC1 17 TYR A 30 SER A 31 GLY A 32 LYS A 33 SITE 2 AC1 17 THR A 34 THR A 35 GLU A 102 ASN A 130 SITE 3 AC1 17 LYS A 131 ASP A 133 LEU A 134 SER A 163 SITE 4 AC1 17 CYS A 164 LYS A 165 HOH A 301 HOH A 342 SITE 5 AC1 17 HOH A 351 CRYST1 118.032 37.374 39.315 90.00 90.00 90.00 P 21 21 2 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 0.008472 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026757 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025436 0.00000