HEADER SIGNALING PROTEIN 17-APR-00 1EUO TITLE CRYSTAL STRUCTURE OF NITROPHORIN 2 (PROLIXIN-S) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITROPHORIN 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROLIXIN-S; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODNIUS PROLIXUS; SOURCE 3 ORGANISM_TAXID: 13249; SOURCE 4 ORGAN: SALIVARY GLAND; SOURCE 5 GENE: SALIVARY GLAND CDNA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET 17B KEYWDS BETA BARREL, LIPOCALIN, HEME, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.F.ANDERSEN,W.R.MONTFORT REVDAT 7 06-NOV-24 1EUO 1 REMARK SEQADV LINK REVDAT 6 18-APR-18 1EUO 1 REMARK REVDAT 5 04-OCT-17 1EUO 1 REMARK REVDAT 4 24-FEB-09 1EUO 1 VERSN REVDAT 3 31-MAY-05 1EUO 1 JRNL REMARK REVDAT 2 27-SEP-00 1EUO 1 HELIX SHEET REMARK REVDAT 1 10-MAY-00 1EUO 0 JRNL AUTH J.F.ANDERSEN,W.R.MONTFORT JRNL TITL THE CRYSTAL STRUCTURE OF NITROPHORIN 2. A TRIFUNCTIONAL JRNL TITL 2 ANTIHEMOSTATIC PROTEIN FROM THE SALIVA OF RHODNIUS PROLIXUS JRNL REF J.BIOL.CHEM. V. 275 30496 2000 JRNL REFN ISSN 0021-9258 JRNL PMID 10884386 JRNL DOI 10.1074/JBC.M002857200 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 11592 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 599 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1411 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 80 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.20 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.270 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 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 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USED SIMULATED ANNEALING AND MAXIMUM REMARK 3 LIKELIHOOD PROCEDURES. REMARK 4 REMARK 4 1EUO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-APR-00. REMARK 100 THE DEPOSITION ID IS D_1000010908. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-OCT-98 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.7 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 : ENRAF-NONIUS 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 : DIFFRACTOMETER REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS FAST REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MADNESS REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12186 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 9.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.5000 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) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 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: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM PHOSPHATE, TRIS-HCL, PH 7.7, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 20.17000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 63.98000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.17000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 63.98000 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 BIOLOGICAL ASSEMBLY IS A MONOMER CONTAINING A SINGLE REMARK 300 HEME PROSTHETIC GROUP. HIS 57 FORMS THE PROXIMAL HEME LIGAND, AND REMARK 300 NH3 FORMS THE DISTAL LIGAND. 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 259 LIES ON A SPECIAL POSITION. 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 ASN A 5 42.67 -99.15 REMARK 500 THR A 35 -50.42 -122.18 REMARK 500 SER A 77 -75.64 -51.18 REMARK 500 ASP A 112 -160.82 -126.35 REMARK 500 GLU A 124 74.26 -116.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 260 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 57 NE2 REMARK 620 2 HEM A 260 NA 96.5 REMARK 620 3 HEM A 260 NB 91.9 89.0 REMARK 620 4 HEM A 260 NC 85.5 178.0 90.8 REMARK 620 5 HEM A 260 ND 88.0 89.5 178.5 90.7 REMARK 620 6 NH3 A 261 N 173.0 90.4 87.3 87.5 93.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 260 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH3 A 261 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NP1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NITROPHORIN 1 REMARK 900 RELATED ID: 1NP4 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF NITROPHORIN 4 DBREF 1EUO A 1 179 UNP Q26241 NP2_RHOPR 24 202 SEQADV 1EUO MET A 0 UNP Q26241 CLONING ARTIFACT SEQRES 1 A 180 MET ASP CYS SER THR ASN ILE SER PRO LYS GLN GLY LEU SEQRES 2 A 180 ASP LYS ALA LYS TYR PHE SER GLY LYS TRP TYR VAL THR SEQRES 3 A 180 HIS PHE LEU ASP LYS ASP PRO GLN VAL THR ASP GLN TYR SEQRES 4 A 180 CYS SER SER PHE THR PRO ARG GLU SER ASP GLY THR VAL SEQRES 5 A 180 LYS GLU ALA LEU TYR HIS TYR ASN ALA ASN LYS LYS THR SEQRES 6 A 180 SER PHE TYR ASN ILE GLY GLU GLY LYS LEU GLU SER SER SEQRES 7 A 180 GLY LEU GLN TYR THR ALA LYS TYR LYS THR VAL ASP LYS SEQRES 8 A 180 LYS LYS ALA VAL LEU LYS GLU ALA ASP GLU LYS ASN SER SEQRES 9 A 180 TYR THR LEU THR VAL LEU GLU ALA ASP ASP SER SER ALA SEQRES 10 A 180 LEU VAL HIS ILE CYS LEU ARG GLU GLY SER LYS ASP LEU SEQRES 11 A 180 GLY ASP LEU TYR THR VAL LEU THR HIS GLN LYS ASP ALA SEQRES 12 A 180 GLU PRO SER ALA LYS VAL LYS SER ALA VAL THR GLN ALA SEQRES 13 A 180 GLY LEU GLN LEU SER GLN PHE VAL GLY THR LYS ASP LEU SEQRES 14 A 180 GLY CYS GLN TYR ASP ASP GLN PHE THR SER LEU HET HEM A 260 43 HET NH3 A 261 1 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM NH3 AMMONIA HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 NH3 H3 N FORMUL 4 HOH *80(H2 O) HELIX 1 1 ASP A 13 PHE A 18 1 6 HELIX 2 2 SER A 145 ALA A 155 1 11 HELIX 3 3 GLN A 158 PHE A 162 5 5 HELIX 4 4 ASP A 174 SER A 178 1 5 SHEET 1 A 9 LYS A 21 ASP A 29 0 SHEET 2 A 9 LYS A 127 THR A 137 -1 O VAL A 135 N THR A 25 SHEET 3 A 9 SER A 115 GLU A 124 -1 N ILE A 120 O LEU A 132 SHEET 4 A 9 ASN A 102 ALA A 111 -1 O THR A 107 N HIS A 119 SHEET 5 A 9 GLN A 80 VAL A 88 -1 N ALA A 83 O TYR A 104 SHEET 6 A 9 SER A 65 LEU A 74 -1 O ILE A 69 N LYS A 86 SHEET 7 A 9 THR A 50 ASN A 59 -1 N LEU A 55 O ASN A 68 SHEET 8 A 9 TYR A 38 SER A 47 -1 N ARG A 45 O LYS A 52 SHEET 9 A 9 LYS A 21 ASP A 29 -1 N VAL A 24 O SER A 40 SSBOND 1 CYS A 2 CYS A 121 1555 1555 2.03 SSBOND 2 CYS A 39 CYS A 170 1555 1555 2.02 LINK NE2 HIS A 57 FE HEM A 260 1555 1555 2.01 LINK FE HEM A 260 N NH3 A 261 1555 1555 2.10 SITE 1 AC1 14 VAL A 24 PHE A 27 TYR A 38 SER A 40 SITE 2 AC1 14 GLU A 53 LEU A 55 HIS A 57 ASN A 68 SITE 3 AC1 14 TYR A 85 THR A 87 TYR A 104 LEU A 132 SITE 4 AC1 14 HOH A 244 NH3 A 261 SITE 1 AC2 2 LEU A 132 HEM A 260 CRYST1 40.340 127.960 33.720 90.00 90.00 90.00 P 21 21 2 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 0.024789 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007815 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029656 0.00000