HEADER TRANSPORT PROTEIN 05-NOV-25 9XKC TITLE CRYSTAL STRUCTURE OF ODORANT BINDING PROTEIN 11 FROM LOCUSTA TITLE 2 MIGRATORIA (LMIGOBP11) WITH ACETATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ODORANT BINDING PROTEIN 11; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACRIDIDAE; SOURCE 3 ORGANISM_TAXID: 7002; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ODORANT-BINDING PROTEIN OBP11 LOCUSTA MIGRATORIA LOCUST, TRANSPORT KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.T.ZHAO,X.J.GUO,J.YE,J.L.CHANG REVDAT 1 11-NOV-26 9XKC 0 JRNL AUTH P.T.ZHAO,X.J.GUO,J.L.CHANG JRNL TITL CRYSTAL STRUCTURE OF ODORANT BINDING PROTEIN 11 FROM LOCUSTA JRNL TITL 2 MIGRATORIA (LMIGOBP11) WITH ACETATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 27633 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.960 REMARK 3 FREE R VALUE TEST SET COUNT : 1371 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 40.4400 - 3.6900 0.98 2716 121 0.1762 0.1867 REMARK 3 2 3.6500 - 2.9100 1.00 2646 145 0.1752 0.2159 REMARK 3 3 2.9100 - 2.5400 1.00 2660 134 0.1901 0.2730 REMARK 3 4 2.5400 - 2.3100 1.00 2604 141 0.1838 0.2298 REMARK 3 5 2.3100 - 2.1400 1.00 2639 132 0.1842 0.2328 REMARK 3 6 2.1400 - 2.0200 1.00 2596 132 0.1843 0.2266 REMARK 3 7 2.0200 - 1.9100 1.00 2609 150 0.1917 0.2587 REMARK 3 8 1.9100 - 1.8300 1.00 2612 133 0.2021 0.2486 REMARK 3 9 1.8300 - 1.7600 1.00 2568 138 0.2335 0.2967 REMARK 3 10 1.7600 - 1.7000 1.00 2612 145 0.2444 0.2777 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.460 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 : 0.008 NULL REMARK 3 ANGLE : 1.004 NULL REMARK 3 CHIRALITY : 0.052 326 REMARK 3 PLANARITY : 0.006 377 REMARK 3 DIHEDRAL : 5.089 286 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 9XKC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 11-NOV-25. REMARK 100 THE DEPOSITION ID IS D_1300049075. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-23 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978530 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 1.0.5 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.7 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32571 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 53.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.81500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE, 25% W/V REMARK 280 POLYETHYLENE GLYCOL 3,350, PH 4.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 18.45450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.07050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.23100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.07050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.45450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.23100 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 HIS B 140 REMARK 465 HIS B 141 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 GLU A 3 70.60 40.15 REMARK 500 CYS A 71 144.12 81.79 REMARK 500 GLU A 139 -151.88 -110.95 REMARK 500 GLU B 33 147.68 -171.66 REMARK 500 REMARK 500 REMARK: NULL DBREF 9XKC A 1 141 PDB 9XKC 9XKC 1 141 DBREF 9XKC B 1 141 PDB 9XKC 9XKC 1 141 SEQRES 1 A 141 MET LEU GLU PRO ASP PHE THR LYS GLY ILE SER ASP VAL SEQRES 2 A 141 LYS ALA CYS MET ALA SER GLU ASN LEU ASP SER LEU ASP SEQRES 3 A 141 ALA LEU ARG THR ASN LYS GLU ALA ARG THR ALA GLU GLU SEQRES 4 A 141 LYS CYS PHE ILE GLY CYS ILE MET LYS PHE VAL GLU VAL SEQRES 5 A 141 LEU ASN SER ASP GLY GLN TYR ASP VAL ALA LEU PHE LYS SEQRES 6 A 141 ASP HIS ILE ASN GLY CYS PRO GLU MET ALA LYS ASP GLN SEQRES 7 A 141 GLN LYS LYS ALA ALA LEU LEU GLU VAL ALA GLU SER CYS SEQRES 8 A 141 ALA GLY LYS ALA SER ALA CYS SER GLY HIS CYS GLU CYS SEQRES 9 A 141 GLY VAL ILE VAL ALA ASN CYS LEU ALA ASP GLU MET GLU SEQRES 10 A 141 ALA LYS GLY GLN GLU THR ILE TYR ASP LEU LEU GLU THR SEQRES 11 A 141 ILE PHE ALA LYS MET ASP ALA LEU GLU HIS HIS SEQRES 1 B 141 MET LEU GLU PRO ASP PHE THR LYS GLY ILE SER ASP VAL SEQRES 2 B 141 LYS ALA CYS MET ALA SER GLU ASN LEU ASP SER LEU ASP SEQRES 3 B 141 ALA LEU ARG THR ASN LYS GLU ALA ARG THR ALA GLU GLU SEQRES 4 B 141 LYS CYS PHE ILE GLY CYS ILE MET LYS PHE VAL GLU VAL SEQRES 5 B 141 LEU ASN SER ASP GLY GLN TYR ASP VAL ALA LEU PHE LYS SEQRES 6 B 141 ASP HIS ILE ASN GLY CYS PRO GLU MET ALA LYS ASP GLN SEQRES 7 B 141 GLN LYS LYS ALA ALA LEU LEU GLU VAL ALA GLU SER CYS SEQRES 8 B 141 ALA GLY LYS ALA SER ALA CYS SER GLY HIS CYS GLU CYS SEQRES 9 B 141 GLY VAL ILE VAL ALA ASN CYS LEU ALA ASP GLU MET GLU SEQRES 10 B 141 ALA LYS GLY GLN GLU THR ILE TYR ASP LEU LEU GLU THR SEQRES 11 B 141 ILE PHE ALA LYS MET ASP ALA LEU GLU HIS HIS HET ACT A 201 4 HETNAM ACT ACETATE ION FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 HOH *274(H2 O) HELIX 1 AA1 ASP A 5 GLU A 20 1 16 HELIX 2 AA2 LEU A 25 LYS A 32 1 8 HELIX 3 AA3 THR A 36 VAL A 50 1 15 HELIX 4 AA4 ASP A 60 GLY A 70 1 11 HELIX 5 AA5 PRO A 72 LYS A 76 5 5 HELIX 6 AA6 ASP A 77 CYS A 91 1 15 HELIX 7 AA7 ALA A 92 ALA A 97 5 6 HELIX 8 AA8 GLY A 100 LYS A 119 1 20 HELIX 9 AA9 THR A 123 LEU A 138 1 16 HELIX 10 AB1 PHE B 6 GLU B 20 1 15 HELIX 11 AB2 LEU B 25 LYS B 32 1 8 HELIX 12 AB3 THR B 36 VAL B 50 1 15 HELIX 13 AB4 ASP B 60 GLY B 70 1 11 HELIX 14 AB5 PRO B 72 LYS B 76 5 5 HELIX 15 AB6 ASP B 77 GLY B 93 1 17 HELIX 16 AB7 SER B 99 LYS B 119 1 21 HELIX 17 AB8 THR B 123 GLU B 139 1 17 SSBOND 1 CYS A 16 CYS A 45 1555 1555 2.05 SSBOND 2 CYS A 41 CYS A 102 1555 1555 2.05 SSBOND 3 CYS A 71 CYS B 71 1555 1555 2.03 SSBOND 4 CYS A 91 CYS A 111 1555 1555 2.04 SSBOND 5 CYS A 98 CYS A 104 1555 1555 2.03 SSBOND 6 CYS B 16 CYS B 45 1555 1555 2.06 SSBOND 7 CYS B 41 CYS B 102 1555 1555 2.06 SSBOND 8 CYS B 91 CYS B 111 1555 1555 2.04 SSBOND 9 CYS B 98 CYS B 104 1555 1555 2.03 CRYST1 36.909 62.462 106.141 90.00 90.00 90.00 P 21 21 21 8 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 0.027094 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016010 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009421 0.00000 CONECT 120 341 CONECT 312 763 CONECT 341 120 CONECT 547 1612 CONECT 697 823 CONECT 737 778 CONECT 763 312 CONECT 778 737 CONECT 823 697 CONECT 1185 1406 CONECT 1377 1828 CONECT 1406 1185 CONECT 1612 547 CONECT 1762 1888 CONECT 1802 1843 CONECT 1828 1377 CONECT 1843 1802 CONECT 1888 1762 CONECT 2111 2112 2113 2114 CONECT 2112 2111 CONECT 2113 2111 CONECT 2114 2111 MASTER 232 0 1 17 0 0 0 6 2386 2 22 22 END