HEADER SIGNALING PROTEIN 19-DEC-00 1HQP TITLE CRYSTAL STRUCTURE OF A TRUNCATED FORM OF PORCINE ODORANT-BINDING TITLE 2 PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ODORANT-BINDING PROTEIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SUS SCROFA; SOURCE 3 ORGANISM_COMMON: PIG; SOURCE 4 ORGANISM_TAXID: 9823; SOURCE 5 TISSUE: NASAL MUCOSA KEYWDS LIPOCALIN, DIMER, LIGAND-BINDING SITE, ACCESS TO THE BINDING SITE, KEYWDS 2 SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.PERDUCA,F.MANCIA,R.DEL GIORGIO,H.L.MONACO REVDAT 4 09-AUG-23 1HQP 1 REMARK REVDAT 3 04-OCT-17 1HQP 1 REMARK REVDAT 2 24-FEB-09 1HQP 1 VERSN REVDAT 1 17-JAN-01 1HQP 0 JRNL AUTH M.PERDUCA,F.MANCIA,R.DEL GIORGIO,H.L.MONACO JRNL TITL CRYSTAL STRUCTURE OF A TRUNCATED FORM OF PORCINE JRNL TITL 2 ODORANT-BINDING PROTEIN. JRNL REF PROTEINS V. 42 201 2001 JRNL REFN ISSN 0887-3585 JRNL PMID 11119644 JRNL DOI 10.1002/1097-0134(20010201)42:2<201::AID-PROT70>3.3.CO;2-Z REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.4 REMARK 3 NUMBER OF REFLECTIONS : 5620 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : R-FREE WAS NOT CALCULATED REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 0 REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 6990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1179 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 37.000 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.004 ; NULL ; NULL REMARK 3 BOND ANGLES (DEGREES) : 1.270 ; NULL ; NULL REMARK 3 TORSION ANGLES (DEGREES) : 16.338; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : NULL ; NULL ; NULL REMARK 3 GENERAL PLANES (A) : NULL ; NULL ; NULL REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS (A) : NULL ; NULL ; NULL REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : ENGH & HUBER REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HQP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-DEC-00. REMARK 100 THE DEPOSITION ID IS D_1000012526. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-92 REMARK 200 TEMPERATURE (KELVIN) : 293.0 REMARK 200 PH : 7.5 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : GRAPHITE MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : XENTRONICS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : X-GEN REMARK 200 DATA SCALING SOFTWARE : X-GEN REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5662 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 80.0 REMARK 200 DATA REDUNDANCY : 2.160 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 64.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.10700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.10 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1A3Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, TRIS, ETHYLENE REMARK 280 GLYCOL, PH 7.5, MICRODIALYSIS, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 44.59000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.07000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.59000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.07000 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 300 REMARK: THE ASYMMETRIC UNIT IS A MONOMER. THE DIMER IS GENERATED BY REMARK 300 THE CRYSTALLOGRAPHIC TWO-FOLD AXIS 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 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 GLN A 1 REMARK 465 GLU A 2 REMARK 465 PRO A 3 REMARK 465 GLN A 4 REMARK 465 PRO A 5 REMARK 465 GLU A 6 REMARK 465 GLN A 7 REMARK 465 ASP A 8 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ALA A 157 C ALA A 157 OXT 1.845 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 156 C - N - CD ANGL. DEV. = -12.9 DEGREES 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 GLN A 36 70.37 -69.51 REMARK 500 ARG A 40 -33.45 -138.16 REMARK 500 ASN A 60 11.10 55.59 REMARK 500 TYR A 82 124.16 176.81 REMARK 500 TYR A 92 154.52 179.56 REMARK 500 GLU A 107 17.81 -68.21 REMARK 500 ASP A 153 95.13 -52.56 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 PRZ A 160 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1A3Y RELATED DB: PDB REMARK 900 1A3Y CONTAINS THE SAME PROTEIN CRYSTALLIZED IN A DIFFERENT SPACE REMARK 900 GROUP AND UNLIGANDED DBREF 1HQP A 1 157 UNP P81245 OBP_PIG 1 157 SEQRES 1 A 157 GLN GLU PRO GLN PRO GLU GLN ASP PRO PHE GLU LEU SER SEQRES 2 A 157 GLY LYS TRP ILE THR SER TYR ILE GLY SER SER ASP LEU SEQRES 3 A 157 GLU LYS ILE GLY GLU ASN ALA PRO PHE GLN VAL PHE MET SEQRES 4 A 157 ARG SER ILE GLU PHE ASP ASP LYS GLU SER LYS VAL TYR SEQRES 5 A 157 LEU ASN PHE PHE SER LYS GLU ASN GLY ILE CYS GLU GLU SEQRES 6 A 157 PHE SER LEU ILE GLY THR LYS GLN GLU GLY ASN THR TYR SEQRES 7 A 157 ASP VAL ASN TYR ALA GLY ASN ASN LYS PHE VAL VAL SER SEQRES 8 A 157 TYR ALA SER GLU THR ALA LEU ILE ILE SER ASN ILE ASN SEQRES 9 A 157 VAL ASP GLU GLU GLY ASP LYS THR ILE MET THR GLY LEU SEQRES 10 A 157 LEU GLY LYS GLY THR ASP ILE GLU ASP GLN ASP LEU GLU SEQRES 11 A 157 LYS PHE LYS GLU VAL THR ARG GLU ASN GLY ILE PRO GLU SEQRES 12 A 157 GLU ASN ILE VAL ASN ILE ILE GLU ARG ASP ASP CYS PRO SEQRES 13 A 157 ALA HET PRZ A 160 12 HETNAM PRZ 2-ISOBUTYL-3-METHOXYPYRAZINE FORMUL 2 PRZ C9 H14 N2 O HELIX 1 1 GLU A 125 ASN A 139 1 15 HELIX 2 2 PRO A 142 ILE A 146 5 5 SHEET 1 A 9 PHE A 38 ASP A 45 0 SHEET 2 A 9 LYS A 50 GLU A 59 -1 O LYS A 50 N ASP A 45 SHEET 3 A 9 ILE A 62 GLN A 73 -1 N ILE A 62 O GLU A 59 SHEET 4 A 9 THR A 77 ASN A 81 -1 O THR A 77 N GLN A 73 SHEET 5 A 9 GLY A 84 ALA A 93 -1 O ASN A 86 N VAL A 80 SHEET 6 A 9 ALA A 97 ASP A 106 -1 N ILE A 99 O TYR A 92 SHEET 7 A 9 LYS A 111 GLY A 119 -1 O THR A 112 N ASN A 104 SHEET 8 A 9 ILE A 17 SER A 23 -1 N ILE A 17 O GLY A 119 SHEET 9 A 9 VAL A 147 ASN A 148 -1 N VAL A 147 O ILE A 21 SSBOND 1 CYS A 63 CYS A 155 1555 1555 2.03 SITE 1 AC1 5 MET A 39 LEU A 53 PHE A 55 VAL A 80 SITE 2 AC1 5 ASN A 102 CRYST1 89.180 44.140 41.240 90.00 107.03 90.00 C 1 2 1 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 0.011213 0.000000 0.003434 0.00000 SCALE2 0.000000 0.022655 -0.000001 0.00000 SCALE3 0.000000 0.000000 0.025360 0.00000