HEADER TRANSPORT PROTEIN 30-DEC-15 5HAE TITLE CRYSTAL STRUCTURE OF LTBP1 LTC4 COMPLEX COLLECTED ON AN IN-HOUSE TITLE 2 SOURCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPOCALIN AI-4; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODNIUS PROLIXUS; SOURCE 3 ORGANISM_COMMON: TRIATOMID BUG; SOURCE 4 ORGANISM_TAXID: 13249; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS LIPOCALIN, SALIVARY, RHODNIUS, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.F.ANDERSEN REVDAT 3 07-MAR-18 5HAE 1 REMARK REVDAT 2 27-JUL-16 5HAE 1 JRNL REVDAT 1 11-MAY-16 5HAE 0 JRNL AUTH W.JABLONKA,V.PHAM,G.NARDONE,A.GITTIS,L.SILVA-CARDOSO, JRNL AUTH 2 G.C.ATELLA,J.M.RIBEIRO,J.F.ANDERSEN JRNL TITL STRUCTURE AND LIGAND-BINDING MECHANISM OF A CYSTEINYL JRNL TITL 2 LEUKOTRIENE-BINDING PROTEIN FROM A BLOOD-FEEDING DISEASE JRNL TITL 3 VECTOR. JRNL REF ACS CHEM.BIOL. V. 11 1934 2016 JRNL REFN ESSN 1554-8937 JRNL PMID 27124118 JRNL DOI 10.1021/ACSCHEMBIO.6B00032 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 9026 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.310 REMARK 3 FREE R VALUE TEST SET COUNT : 479 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 34.9914 - 2.8864 0.98 2933 164 0.1383 0.1799 REMARK 3 2 2.8864 - 2.2912 0.97 2839 161 0.1625 0.2206 REMARK 3 3 2.2912 - 2.0016 0.94 2775 154 0.1455 0.2395 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.31 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.70 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 : 0.006 1256 REMARK 3 ANGLE : 1.104 1689 REMARK 3 CHIRALITY : 0.042 183 REMARK 3 PLANARITY : 0.004 220 REMARK 3 DIHEDRAL : 16.538 456 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): -6.1287 5.8651 -9.9589 REMARK 3 T TENSOR REMARK 3 T11: 0.0867 T22: 0.0989 REMARK 3 T33: 0.0964 T12: 0.0019 REMARK 3 T13: -0.0050 T23: -0.0125 REMARK 3 L TENSOR REMARK 3 L11: 1.3659 L22: 1.4074 REMARK 3 L33: 2.7765 L12: -0.1040 REMARK 3 L13: -0.3517 L23: -0.1903 REMARK 3 S TENSOR REMARK 3 S11: -0.0579 S12: -0.0378 S13: 0.0115 REMARK 3 S21: 0.0533 S22: 0.0243 S23: -0.0358 REMARK 3 S31: 0.0622 S32: 0.0006 S33: 0.0265 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 5HAE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000216752. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7-8 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 FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9042 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.13600 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, PH 8, 30% PEG 6000, PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING 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 29.19400 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 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 TOTAL BURIED SURFACE AREA: 460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL 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 ALA A 1 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 HOH A 405 O HOH A 425 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 TYR A 102 -41.65 69.19 REMARK 500 ASN A 104 -54.10 -132.93 REMARK 500 GLU A 133 -138.81 -128.13 REMARK 500 LEU A 147 59.88 -102.03 REMARK 500 LEU A 153 -145.53 -97.96 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 EAH A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GSH A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5H9L RELATED DB: PDB REMARK 900 RELATED ID: 5H9N RELATED DB: PDB REMARK 900 RELATED ID: 5HA0 RELATED DB: PDB DBREF 5HAE A 1 156 UNP Q7YT09 Q7YT09_RHOPR 18 173 SEQRES 1 A 156 ALA GLU VAL THR SER ILE PRO THR GLY CYS ASN ALA LEU SEQRES 2 A 156 SER GLY LYS ILE MET SER GLY PHE ASP ALA ASN ARG PHE SEQRES 3 A 156 PHE THR GLY ASP TRP TYR LEU THR HIS SER ARG ASP SER SEQRES 4 A 156 GLU VAL PRO VAL ARG CYS GLU LYS TYR GLN THR GLY SER SEQRES 5 A 156 ASN LEU GLN LEU ASN PHE ASN GLY LYS ASN GLY ASP VAL SEQRES 6 A 156 LYS CYS SER GLY SER THR VAL SER GLY ASN GLN GLY PHE SEQRES 7 A 156 TYR SER PHE GLN CYS THR THR THR SER GLY GLY SER PHE SEQRES 8 A 156 THR SER TYR MET ALA VAL VAL GLU THR ASP TYR ALA ASN SEQRES 9 A 156 TYR ALA LEU LEU TYR ARG CYS GLY LEU TYR GLY SER THR SEQRES 10 A 156 THR PRO LYS ASP ASN PHE LEU LEU PHE ASN ARG GLN SER SEQRES 11 A 156 SER GLY GLU ILE PRO ALA GLY LEU SER THR LYS LEU ASN SEQRES 12 A 156 GLN LEU GLU LEU THR SER LEU ASN LYS LEU GLY CYS SER HET EAH A 201 23 HET GSH A 202 20 HETNAM EAH (5S,7E,9E,11Z,14Z)-5-HYDROXYICOSA-7,9,11,14-TETRAENOIC HETNAM 2 EAH ACID HETNAM GSH GLUTATHIONE FORMUL 2 EAH C20 H32 O3 FORMUL 3 GSH C10 H17 N3 O6 S FORMUL 4 HOH *168(H2 O) HELIX 1 AA1 ASP A 22 PHE A 27 1 6 HELIX 2 AA2 PRO A 135 GLY A 137 5 3 HELIX 3 AA3 LEU A 138 LEU A 145 1 8 SHEET 1 AA110 ASN A 151 LYS A 152 0 SHEET 2 AA110 ASP A 30 SER A 36 -1 N SER A 36 O ASN A 151 SHEET 3 AA110 LYS A 120 ASN A 127 -1 O ASN A 127 N TYR A 32 SHEET 4 AA110 TYR A 105 GLY A 112 -1 N LEU A 108 O LEU A 124 SHEET 5 AA110 SER A 90 THR A 100 -1 N GLU A 99 O LEU A 107 SHEET 6 AA110 PHE A 78 THR A 85 -1 N CYS A 83 O PHE A 91 SHEET 7 AA110 GLY A 63 THR A 71 -1 N SER A 70 O SER A 80 SHEET 8 AA110 GLN A 55 GLY A 60 -1 N PHE A 58 O VAL A 65 SHEET 9 AA110 GLU A 46 GLY A 51 -1 N GLN A 49 O ASN A 57 SHEET 10 AA110 ASP A 30 SER A 36 -1 N TRP A 31 O TYR A 48 SSBOND 1 CYS A 10 CYS A 111 1555 1555 2.03 SSBOND 2 CYS A 45 CYS A 155 1555 1555 2.04 SSBOND 3 CYS A 67 CYS A 83 1555 1555 2.03 CISPEP 1 VAL A 41 PRO A 42 0 -4.55 SITE 1 AC1 12 LEU A 56 PHE A 58 LYS A 61 PHE A 91 SITE 2 AC1 12 SER A 93 ARG A 110 TYR A 114 ASN A 122 SITE 3 AC1 12 GSH A 202 HOH A 306 HOH A 330 HOH A 331 SITE 1 AC2 15 ASP A 22 ALA A 23 ASN A 24 GLY A 60 SITE 2 AC2 15 LYS A 61 VAL A 65 PHE A 91 TYR A 114 SITE 3 AC2 15 EAH A 201 HOH A 310 HOH A 313 HOH A 314 SITE 4 AC2 15 HOH A 335 HOH A 389 HOH A 397 CRYST1 34.269 58.388 36.018 90.00 103.75 90.00 P 1 21 1 2 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 0.029181 0.000000 0.007139 0.00000 SCALE2 0.000000 0.017127 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028583 0.00000