HEADER TRANSPORT PROTEIN 03-MAY-01 1IKH OBSLTE 09-JAN-02 1IKH 1KOI TITLE CRYSTAL STRUCTURE OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS TITLE 2 COMPLEXED WITH NITRIC OXIDE AT 1.08 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITROPHORIN 4; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: NITRIC OXIDE OCCUPIES THE SIXTH COMPND 6 COORDINATION POSITION OF THE IRON. THE HEME IS DISORDERED COMPND 7 BY A ROTATION OF 180 DEGREES AROUND THE CHA-FE-CHC AXIS. COMPND 8 THE ONLY EVIDENCE OF THIS DISORDER IS THE APPEARANCE OF COMPND 9 METHYL GROUPS CMB AND CMC AS VINYLS. THESE EXTRA ATOMS ARE COMPND 10 CALLED CBBB AND CBCB. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODNIUS PROLIXUS; SOURCE 3 ORGANISM_COMMON: KISSING BUG; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-17B-NP4 KEYWDS NITRIC OXIDE TRANSPORT, FERRIC HEME, ANITHISTIMINE, KEYWDS 2 LIPOCALIN EXPDTA X-RAY DIFFRACTION AUTHOR S.A.ROBERTS,A.WEICHSEL,Y.QIU,J.A.SHELNUTT,F.A.WALKER, AUTHOR 2 W.R.MONTFORT REVDAT 3 26-JUN-02 1IKH 1 OBSLTE REVDAT 2 09-JAN-01 1IKH 1 OBSLTE REVDAT 1 03-OCT-01 1IKH 0 JRNL AUTH S.A.ROBERTS,A.WEICHSEL,Y.QIU,J.A.SHELNUTT, JRNL AUTH 2 F.A.WALKER,W.R.MONTFORT JRNL TITL LIGAND-INDUCED HEME RUFFLING AND BENT NO GEOMETRY JRNL TITL 2 IN ULTRA-HIGH RESOLUTION STRUCTURES OF NITROPHORIN JRNL TITL 3 4 JRNL REF BIOCHEMISTRY V. 40 11327 2001 JRNL REFN ASTM BICHAW US ISSN 0006-2960 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.08 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.08 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.117 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.117 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.147 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3144 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 62726 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1452 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 264 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 ANGLE DISTANCES (A) : NULL REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SHELX CONJUGATE GRADIENT REFINEMENT. REMARK 3 HYDROGEN ATOMS ADDED AT CALCULATED POSITIONS. HEME AND IRON REMARK 3 COORDINATION SPHERE REFINED WITHOUT RESTRAINTS. REMARK 4 REMARK 4 1IKH COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-MAY-2001. REMARK 100 THE RCSB ID CODE IS RCSB013364. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-2000 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.975 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59582 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.08 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.24000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 15.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1ERX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, SODIUM CITRATE, PH 5.6, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 1/2+X,1/2+Y,Z REMARK 290 4555 1/2-X,1/2+Y,-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 35.07450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.20950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.07450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.20950 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 299 LIES ON A SPECIAL POSITION. REMARK 375 HOH 378 LIES ON A SPECIAL POSITION. REMARK 375 HOH 437 LIES ON A SPECIAL POSITION. 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 14 CG - CD - CE ANGL. DEV. = 14.5 DEGREES REMARK 500 LYS A 14 CG - CD - CE ANGL. DEV. = 16.2 DEGREES REMARK 500 LYS A 148 CG - CD - CE ANGL. DEV. = 14.3 DEGREES REMARK 500 CYS A 171 C - N - CA ANGL. DEV. =-16.6 DEGREES DBREF 1IKH A 1 184 UNP Q94734 NP4_RHOPR 22 205 SEQRES 1 A 184 ALA CYS THR LYS ASN ALA ILE ALA GLN THR GLY PHE ASN SEQRES 2 A 184 LYS ASP LYS TYR PHE ASN GLY ASP VAL TRP TYR VAL THR SEQRES 3 A 184 ASP TYR LEU ASP LEU GLU PRO ASP ASP VAL PRO LYS ARG SEQRES 4 A 184 TYR CYS ALA ALA LEU ALA ALA GLY THR ALA SER GLY LYS SEQRES 5 A 184 LEU LYS GLU ALA LEU TYR HIS TYR ASP PRO LYS THR GLN SEQRES 6 A 184 ASP THR PHE TYR ASP VAL SER GLU LEU GLN VAL GLU SER SEQRES 7 A 184 LEU GLY LYS TYR THR ALA ASN PHE LYS LYS VAL ASP LYS SEQRES 8 A 184 ASN GLY ASN VAL LYS VAL ALA VAL THR ALA GLY ASN TYR SEQRES 9 A 184 TYR THR PHE THR VAL MET TYR ALA ASP ASP SER SER ALA SEQRES 10 A 184 LEU ILE HIS THR CYS LEU HIS LYS GLY ASN LYS ASP LEU SEQRES 11 A 184 GLY ASP LEU TYR ALA VAL LEU ASN ARG ASN LYS ASP ALA SEQRES 12 A 184 ALA ALA GLY ASP LYS VAL LYS SER ALA VAL SER ALA ALA SEQRES 13 A 184 THR LEU GLU PHE SER LYS PHE ILE SER THR LYS GLU ASN SEQRES 14 A 184 ASN CYS ALA TYR ASP ASN ASP SER LEU LYS SER LEU LEU SEQRES 15 A 184 THR LYS HET HEM A 185 45 HET NO 186 2 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM NO NITROGEN OXIDE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 NO N O FORMUL 4 HOH *264(H2 O1) HELIX 1 1 ASN A 13 PHE A 18 1 6 HELIX 2 2 GLU A 32 VAL A 36 5 5 HELIX 3 3 GLY A 146 ALA A 156 1 11 HELIX 4 4 GLU A 159 PHE A 163 5 5 HELIX 5 5 ASP A 174 LEU A 182 1 9 SHEET 1 A10 ASN A 19 ASP A 30 0 SHEET 2 A10 CYS A 41 ALA A 49 -1 O ALA A 42 N VAL A 25 SHEET 3 A10 LYS A 52 TYR A 60 -1 O LYS A 52 N ALA A 49 SHEET 4 A10 THR A 67 SER A 78 -1 O PHE A 68 N HIS A 59 SHEET 5 A10 LYS A 81 VAL A 89 -1 O LYS A 81 N GLU A 77 SHEET 6 A10 ASN A 103 ALA A 112 -1 O ASN A 103 N PHE A 86 SHEET 7 A10 SER A 116 LYS A 125 -1 N LEU A 118 O TYR A 111 SHEET 8 A10 LEU A 133 ASN A 138 -1 O LEU A 133 N THR A 121 SHEET 9 A10 ASN A 19 ASP A 30 -1 N TYR A 24 O ASN A 138 SHEET 10 A10 ILE A 164 SER A 165 -1 N ILE A 164 O TYR A 28 SHEET 11 A10 LYS A 81 VAL A 89 0 SHEET 12 A10 VAL A 95 VAL A 97 -1 N LYS A 96 O LYS A 88 SSBOND 1 CYS A 2 CYS A 122 SSBOND 2 CYS A 41 CYS A 171 LINK N NO 186 FE HEM A 185 LINK NE2 HIS A 59 FE HEM A 185 CRYST1 70.149 42.419 52.942 90.00 94.22 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 0.014255 0.000000 0.001052 0.00000 SCALE2 0.000000 0.023574 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018940 0.00000