HEADER TRANSPORT PROTEIN 29-DEC-15 5HA0 TITLE CRYSTAL STRUCTURE OF THE LTBP1 LEUKOTRIENE D4 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPOCALIN AI-4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 18-173; COMPND 5 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS KEYWDS LIPOCALIN, LEUKOTRIENE, RHODNIUS, SALIVARY, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.F.ANDERSEN REVDAT 3 27-SEP-23 5HA0 1 REMARK REVDAT 2 27-JUL-16 5HA0 1 JRNL REVDAT 1 11-MAY-16 5HA0 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. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.36 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 24696 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.820 REMARK 3 FREE R VALUE TEST SET COUNT : 1190 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 33.3688 - 2.9962 0.99 2671 131 0.1454 0.1695 REMARK 3 2 2.9962 - 2.3783 0.99 2651 129 0.1732 0.1821 REMARK 3 3 2.3783 - 2.0778 0.99 2629 126 0.1585 0.1967 REMARK 3 4 2.0778 - 1.8878 0.99 2615 133 0.1568 0.1930 REMARK 3 5 1.8878 - 1.7525 0.99 2620 140 0.1640 0.2050 REMARK 3 6 1.7525 - 1.6492 0.99 2600 137 0.1667 0.1912 REMARK 3 7 1.6492 - 1.5666 0.99 2599 135 0.1681 0.2213 REMARK 3 8 1.5666 - 1.4984 0.99 2575 144 0.1663 0.2061 REMARK 3 9 1.4984 - 1.4407 0.96 2546 115 0.1794 0.1843 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.35 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.85 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 1253 REMARK 3 ANGLE : 1.080 1686 REMARK 3 CHIRALITY : 0.040 184 REMARK 3 PLANARITY : 0.004 223 REMARK 3 DIHEDRAL : 13.074 453 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): -6.2796 5.9056 -10.0547 REMARK 3 T TENSOR REMARK 3 T11: 0.0594 T22: 0.0606 REMARK 3 T33: 0.0617 T12: 0.0027 REMARK 3 T13: -0.0072 T23: -0.0102 REMARK 3 L TENSOR REMARK 3 L11: 0.8893 L22: 1.2438 REMARK 3 L33: 2.3673 L12: 0.1577 REMARK 3 L13: -0.3351 L23: -0.1686 REMARK 3 S TENSOR REMARK 3 S11: -0.0437 S12: -0.0280 S13: -0.0182 REMARK 3 S21: 0.0537 S22: 0.0198 S23: -0.0282 REMARK 3 S31: 0.0797 S32: -0.0348 S33: 0.0206 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 5HA0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-16. REMARK 100 THE DEPOSITION ID IS D_1000216725. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-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) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300-HS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24723 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.24700 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: 5H9L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8, 30 % PEG 6000, VAPOR REMARK 280 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 29.14950 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 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: 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 459 O HOH A 518 2.15 REMARK 500 O HOH A 388 O HOH A 408 2.16 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 -40.45 71.05 REMARK 500 ASN A 104 -51.08 -133.40 REMARK 500 GLU A 133 -143.20 -125.21 REMARK 500 LEU A 147 60.07 -109.43 REMARK 500 LEU A 153 -144.74 -96.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 526 DISTANCE = 6.43 ANGSTROMS REMARK 525 HOH A 527 DISTANCE = 6.46 ANGSTROMS REMARK 525 HOH A 528 DISTANCE = 6.80 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LTD A 201 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: 5HAE RELATED DB: PDB DBREF 5HA0 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 LTD A 201 34 HETNAM LTD (5~{S},6~{R},7~{E},9~{E},11~{Z},14~{Z})-6-[(2~{R})-2- HETNAM 2 LTD AZANYL-3-(2-HYDROXY-2-OXOETHYLAMINO)-3-OXIDANYLIDENE- HETNAM 3 LTD PROPYL]SULFANYL-5-OXIDANYL-ICOSA-7,9,11,14-TETRAENOIC HETNAM 4 LTD ACID FORMUL 2 LTD C25 H40 N2 O6 S FORMUL 3 HOH *228(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 ALA A 106 O PHE A 126 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 PHE A 81 O SER A 93 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 2.03 SSBOND 3 CYS A 67 CYS A 83 1555 1555 2.05 CISPEP 1 VAL A 41 PRO A 42 0 -3.40 SITE 1 AC1 16 LEU A 56 PHE A 58 GLY A 60 LYS A 61 SITE 2 AC1 16 PHE A 91 SER A 93 MET A 95 ARG A 110 SITE 3 AC1 16 ASN A 122 HOH A 317 HOH A 320 HOH A 329 SITE 4 AC1 16 HOH A 334 HOH A 354 HOH A 356 HOH A 406 CRYST1 34.402 58.299 36.039 90.00 104.14 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 0.029068 0.000000 0.007322 0.00000 SCALE2 0.000000 0.017153 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028615 0.00000