HEADER LIPID BINDING PROTEIN 28-NOV-23 8X8U TITLE CRYSTAL STRUCTURE OF F.OCCIDENTALIS GABARAP COMPND MOL_ID: 1; COMPND 2 MOLECULE: GAMMA-AMINOBUTYRIC ACID RECEPTOR-ASSOCIATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FRANKLINIELLA OCCIDENTALIS; SOURCE 3 ORGANISM_COMMON: WESTERN FLOWER THRIPS; SOURCE 4 ORGANISM_TAXID: 133901; SOURCE 5 GENE: LOC113211372; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LIPID TRANSPORT, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.Q.ZHANG,X.LUO,Z.L.WU,K.H.ZHAO,X.Y.LI REVDAT 1 04-DEC-24 8X8U 0 JRNL AUTH S.Q.ZHANG,X.LUO,Z.L.WU,K.H.ZHAO,X.Y.LI JRNL TITL CRYSTAL STRUCTURE OF F.OCCIDENTALIS GABARAP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 21204 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.470 REMARK 3 FREE R VALUE TEST SET COUNT : 2008 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 26.9500 - 3.8500 0.99 1410 141 0.1493 0.1728 REMARK 3 2 3.8500 - 3.0500 1.00 1386 146 0.1651 0.2232 REMARK 3 3 3.0500 - 2.6700 1.00 1375 142 0.1873 0.2224 REMARK 3 4 2.6700 - 2.4300 1.00 1370 145 0.1731 0.2161 REMARK 3 5 2.4200 - 2.2500 1.00 1382 133 0.1787 0.2008 REMARK 3 6 2.2500 - 2.1200 1.00 1382 146 0.1698 0.1926 REMARK 3 7 2.1200 - 2.0100 1.00 1365 137 0.1706 0.1683 REMARK 3 8 2.0100 - 1.9200 1.00 1337 144 0.1692 0.1987 REMARK 3 9 1.9200 - 1.8500 1.00 1370 152 0.1670 0.2408 REMARK 3 10 1.8500 - 1.7900 1.00 1384 144 0.1963 0.2314 REMARK 3 11 1.7900 - 1.7300 1.00 1343 151 0.2205 0.2552 REMARK 3 12 1.7300 - 1.6800 1.00 1339 143 0.2486 0.2652 REMARK 3 13 1.6800 - 1.6400 1.00 1373 151 0.2258 0.2673 REMARK 3 14 1.6400 - 1.6000 0.99 1380 133 0.2652 0.2743 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 : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.130 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 : 0.011 1018 REMARK 3 ANGLE : 1.165 1369 REMARK 3 CHIRALITY : 0.066 140 REMARK 3 PLANARITY : 0.012 176 REMARK 3 DIHEDRAL : 5.639 133 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 11.0053 17.7616 26.6962 REMARK 3 T TENSOR REMARK 3 T11: 0.2048 T22: 0.2172 REMARK 3 T33: 0.2471 T12: 0.0131 REMARK 3 T13: -0.0035 T23: -0.0005 REMARK 3 L TENSOR REMARK 3 L11: 2.0573 L22: 2.5775 REMARK 3 L33: 2.1635 L12: 0.4523 REMARK 3 L13: -0.5760 L23: -1.3801 REMARK 3 S TENSOR REMARK 3 S11: 0.0049 S12: -0.0303 S13: -0.1211 REMARK 3 S21: -0.0596 S22: 0.0784 S23: 0.2782 REMARK 3 S31: 0.0506 S32: -0.1035 S33: -0.0002 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 8X8U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1300042721. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL10U2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21204 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 26.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.70300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX (1.20.1_4487: ???) REMARK 200 STARTING MODEL: 1GNU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M NA REMARK 280 CITRATE TRIBASIC DIHYDRATE PH5.6, 24% W/V POLYETHYLENE GLYCOL REMARK 280 4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 27.83250 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 13.91625 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 41.74875 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 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 111 -155.74 -99.72 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8X8U A 1 118 UNP A0A6J1T1Q2_FRAOC DBREF2 8X8U A A0A6J1T1Q2 1 118 SEQRES 1 A 118 MET LYS PHE GLN TYR LYS GLU GLU HIS PRO PHE GLU LYS SEQRES 2 A 118 ARG LYS SER GLU GLY GLU LYS ILE ARG ARG LYS TYR PRO SEQRES 3 A 118 ASP ARG VAL PRO VAL ILE VAL GLU LYS ALA PRO LYS ALA SEQRES 4 A 118 ARG ILE GLY ASP LEU ASP LYS LYS LYS TYR LEU VAL PRO SEQRES 5 A 118 SER ASP LEU THR VAL GLY GLN PHE TYR PHE LEU ILE ARG SEQRES 6 A 118 LYS ARG ILE HIS LEU ARG PRO GLU ASP ALA LEU PHE PHE SEQRES 7 A 118 LEU VAL ASN SER VAL VAL PRO PRO SER SER ALA THR MET SEQRES 8 A 118 GLY SER LEU TYR GLN GLU HIS HIS GLU GLU ASP PHE PHE SEQRES 9 A 118 LEU TYR ILE ALA TYR SER ASP GLU ASN VAL TYR GLY LYS SEQRES 10 A 118 LEU FORMUL 2 HOH *88(H2 O) HELIX 1 AA1 PHE A 3 HIS A 9 1 7 HELIX 2 AA2 PRO A 10 TYR A 25 1 16 HELIX 3 AA3 THR A 56 ILE A 68 1 13 HELIX 4 AA4 THR A 90 HIS A 99 1 10 SHEET 1 AA1 4 LYS A 48 PRO A 52 0 SHEET 2 AA1 4 ARG A 28 LYS A 35 -1 N VAL A 31 O TYR A 49 SHEET 3 AA1 4 LEU A 105 SER A 110 1 O LEU A 105 N ILE A 32 SHEET 4 AA1 4 PHE A 77 LEU A 79 -1 N LEU A 79 O ALA A 108 CRYST1 53.901 53.901 55.665 90.00 90.00 90.00 P 41 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 0.018553 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018553 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017965 0.00000 MASTER 234 0 0 4 4 0 0 6 1079 1 0 10 END