HEADER TRANSPORT PROTEIN 17-AUG-12 4GNW TITLE CRYSTAL STRUCTURE OF NITROPHORIN 4 TRIPLE MUTANT COMPLEX WITH AMMONIA COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITROPHORIN-4; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NP4; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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: BL21DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS BETA BARREL, LIPOCALIN, FERRIC HEME, NITRIC OXIDE TRANSPORT, NITRIC KEYWDS 2 OXIDE BINDING, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.WEICHSEL,A.V.ISSAIAN,W.R.MONTFORT REVDAT 2 13-SEP-23 4GNW 1 REMARK SEQADV LINK REVDAT 1 18-SEP-13 4GNW 0 JRNL AUTH V.A.ISSAIAN,A.WEICHSEL,W.R.MONTFORT JRNL TITL CRYSTAL STRUCTURES OF NITROPHORIN 4 TRIPLE MUTANT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.F.ANDRESEN,A.WEICHSEL,C.A.BALFOUR,D.E.CHAMPAGNE, REMARK 1 AUTH 2 W.R.MONTFORT REMARK 1 TITL THE CRYSTAL STRUCTURE OF NITROPHORIN 4 AT 1.5 A RESOLUTION: REMARK 1 TITL 2 TRANSPORT OF NITRIC OXIDE BY A LIPOCALIN-BASED HEME PROTEIN REMARK 1 REF STRUCTURE V. 6 1315 1998 REMARK 1 REFN ISSN 0969-2126 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 133362 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 7000 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.15 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8638 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.3900 REMARK 3 BIN FREE R VALUE SET COUNT : 427 REMARK 3 BIN FREE R VALUE : 0.3990 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2856 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 98 REMARK 3 SOLVENT ATOMS : 449 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.14000 REMARK 3 B22 (A**2) : 0.14000 REMARK 3 B33 (A**2) : -0.21000 REMARK 3 B12 (A**2) : 0.07000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.038 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.036 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.025 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.246 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.974 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3524 ; 0.014 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2230 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4877 ; 1.600 ; 2.021 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5500 ; 0.919 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 446 ; 7.093 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 149 ;39.527 ;25.973 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 576 ;13.649 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;12.122 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 500 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4127 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 745 ; 0.008 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 5754 ; 3.468 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 94 ;23.950 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5995 ; 9.805 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4GNW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000074419. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : DIMOND (111) DOUBLE-CRYSTAL REMARK 200 OPTICS : BENT SI-MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 140391 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 60.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.50700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1NP4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.85 M AMMONIUM PHOSPHATE, 100 MM REMARK 280 TRIS.HCL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.22533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 94.45067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 94.45067 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 47.22533 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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: 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 PHE B 18 55.75 -92.05 REMARK 500 SER B 50 32.16 72.36 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 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 59 NE2 REMARK 620 2 HEM A 201 NA 99.1 REMARK 620 3 HEM A 201 NB 96.4 88.3 REMARK 620 4 HEM A 201 NC 98.6 162.3 90.0 REMARK 620 5 HEM A 201 ND 95.0 87.9 168.4 90.3 REMARK 620 6 NH3 A 202 N 178.1 79.0 84.1 83.2 84.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 59 NE2 REMARK 620 2 HEM A 201 NA 96.0 REMARK 620 3 HEM A 201 NB 92.8 89.6 REMARK 620 4 HEM A 201 NC 94.1 169.9 90.2 REMARK 620 5 HEM A 201 ND 91.4 89.1 175.6 90.4 REMARK 620 6 NH3 A 202 N 179.0 83.2 87.7 86.7 88.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 59 NE2 REMARK 620 2 HEM B 201 NA 83.3 REMARK 620 3 HEM B 201 NB 93.7 88.5 REMARK 620 4 HEM B 201 NC 79.5 162.8 91.2 REMARK 620 5 HEM B 201 ND 84.8 89.1 177.3 90.7 REMARK 620 6 NH3 B 202 N 177.5 97.1 88.8 100.0 92.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 59 NE2 REMARK 620 2 HEM B 201 NA 80.9 REMARK 620 3 HEM B 201 NB 91.2 86.3 REMARK 620 4 HEM B 201 NC 79.0 159.7 90.9 REMARK 620 5 HEM B 201 ND 84.4 88.8 173.8 92.4 REMARK 620 6 NH3 B 202 N 178.2 97.3 89.1 102.8 95.2 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH3 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH3 B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NP4 RELATED DB: PDB REMARK 900 WILD-TYPE NITROPHORIN 4 AMMONIA COMPLEX, MONOCLINIC CRYSTAL FORM DBREF 4GNW A 1 184 UNP Q94734 NP4_RHOPR 22 205 DBREF 4GNW B 1 184 UNP Q94734 NP4_RHOPR 22 205 SEQADV 4GNW ASN A 30 UNP Q94734 ASP 51 ENGINEERED MUTATION SEQADV 4GNW GLN A 32 UNP Q94734 GLU 53 ENGINEERED MUTATION SEQADV 4GNW ASN A 35 UNP Q94734 ASP 56 ENGINEERED MUTATION SEQADV 4GNW ASN B 30 UNP Q94734 ASP 51 ENGINEERED MUTATION SEQADV 4GNW GLN B 32 UNP Q94734 GLU 53 ENGINEERED MUTATION SEQADV 4GNW ASN B 35 UNP Q94734 ASP 56 ENGINEERED MUTATION 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 ASN LEU GLN PRO ASP ASN 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 SEQRES 1 B 184 ALA CYS THR LYS ASN ALA ILE ALA GLN THR GLY PHE ASN SEQRES 2 B 184 LYS ASP LYS TYR PHE ASN GLY ASP VAL TRP TYR VAL THR SEQRES 3 B 184 ASP TYR LEU ASN LEU GLN PRO ASP ASN VAL PRO LYS ARG SEQRES 4 B 184 TYR CYS ALA ALA LEU ALA ALA GLY THR ALA SER GLY LYS SEQRES 5 B 184 LEU LYS GLU ALA LEU TYR HIS TYR ASP PRO LYS THR GLN SEQRES 6 B 184 ASP THR PHE TYR ASP VAL SER GLU LEU GLN VAL GLU SER SEQRES 7 B 184 LEU GLY LYS TYR THR ALA ASN PHE LYS LYS VAL ASP LYS SEQRES 8 B 184 ASN GLY ASN VAL LYS VAL ALA VAL THR ALA GLY ASN TYR SEQRES 9 B 184 TYR THR PHE THR VAL MET TYR ALA ASP ASP SER SER ALA SEQRES 10 B 184 LEU ILE HIS THR CYS LEU HIS LYS GLY ASN LYS ASP LEU SEQRES 11 B 184 GLY ASP LEU TYR ALA VAL LEU ASN ARG ASN LYS ASP ALA SEQRES 12 B 184 ALA ALA GLY ASP LYS VAL LYS SER ALA VAL SER ALA ALA SEQRES 13 B 184 THR LEU GLU PHE SER LYS PHE ILE SER THR LYS GLU ASN SEQRES 14 B 184 ASN CYS ALA TYR ASP ASN ASP SER LEU LYS SER LEU LEU SEQRES 15 B 184 THR LYS HET HEM A 201 88 HET NH3 A 202 1 HET PO4 A 203 5 HET HEM B 201 87 HET NH3 B 202 1 HET PO4 B 203 5 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM NH3 AMMONIA HETNAM PO4 PHOSPHATE ION HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 NH3 2(H3 N) FORMUL 5 PO4 2(O4 P 3-) FORMUL 9 HOH *449(H2 O) HELIX 1 1 ASN A 13 PHE A 18 1 6 HELIX 2 2 GLN 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 LYS A 167 ASN A 170 5 4 HELIX 6 6 ASP A 174 LEU A 181 1 8 HELIX 7 7 LEU A 182 LYS A 184 5 3 HELIX 8 8 ASN B 13 PHE B 18 1 6 HELIX 9 9 GLN B 32 VAL B 36 5 5 HELIX 10 10 GLY B 146 ALA B 156 1 11 HELIX 11 11 GLU B 159 PHE B 163 5 5 HELIX 12 12 ASP B 174 LEU B 181 1 8 SHEET 1 A 7 VAL A 95 VAL A 97 0 SHEET 2 A 7 LYS A 87 VAL A 89 -1 N LYS A 88 O LYS A 96 SHEET 3 A 7 THR A 67 SER A 78 -1 N VAL A 71 O LYS A 87 SHEET 4 A 7 LYS A 52 TYR A 60 -1 N GLU A 55 O SER A 72 SHEET 5 A 7 CYS A 41 ALA A 49 -1 N GLY A 47 O LYS A 54 SHEET 6 A 7 VAL A 22 ASN A 30 -1 N TRP A 23 O LEU A 44 SHEET 7 A 7 ILE A 164 SER A 165 -1 O ILE A 164 N TYR A 28 SHEET 1 B 9 VAL A 95 VAL A 97 0 SHEET 2 B 9 LYS A 87 VAL A 89 -1 N LYS A 88 O LYS A 96 SHEET 3 B 9 THR A 67 SER A 78 -1 N VAL A 71 O LYS A 87 SHEET 4 B 9 LYS A 81 ASN A 85 -1 O THR A 83 N GLN A 75 SHEET 5 B 9 ASN A 103 ALA A 112 -1 O TYR A 105 N ALA A 84 SHEET 6 B 9 SER A 116 LYS A 125 -1 O HIS A 124 N TYR A 104 SHEET 7 B 9 LYS A 128 ASN A 138 -1 O LYS A 128 N LYS A 125 SHEET 8 B 9 VAL A 22 ASN A 30 -1 N LEU A 29 O TYR A 134 SHEET 9 B 9 ILE A 164 SER A 165 -1 O ILE A 164 N TYR A 28 SHEET 1 C11 GLN B 75 SER B 78 0 SHEET 2 C11 LYS B 81 ALA B 84 -1 O LYS B 81 N GLU B 77 SHEET 3 C11 ASN B 103 ALA B 112 -1 O TYR B 105 N ALA B 84 SHEET 4 C11 SER B 116 LYS B 125 -1 O HIS B 124 N TYR B 104 SHEET 5 C11 LYS B 128 ASN B 138 -1 O LEU B 137 N ALA B 117 SHEET 6 C11 ASN B 19 ASN B 30 -1 N TYR B 24 O ASN B 138 SHEET 7 C11 CYS B 41 THR B 48 -1 O LEU B 44 N TRP B 23 SHEET 8 C11 LEU B 53 TYR B 60 -1 O ALA B 56 N ALA B 45 SHEET 9 C11 THR B 67 GLU B 73 -1 O ASP B 70 N LEU B 57 SHEET 10 C11 PHE B 86 VAL B 89 -1 O LYS B 87 N VAL B 71 SHEET 11 C11 VAL B 95 VAL B 97 -1 O LYS B 96 N LYS B 88 SHEET 1 D 7 GLN B 75 SER B 78 0 SHEET 2 D 7 LYS B 81 ALA B 84 -1 O LYS B 81 N GLU B 77 SHEET 3 D 7 ASN B 103 ALA B 112 -1 O TYR B 105 N ALA B 84 SHEET 4 D 7 SER B 116 LYS B 125 -1 O HIS B 124 N TYR B 104 SHEET 5 D 7 LYS B 128 ASN B 138 -1 O LEU B 137 N ALA B 117 SHEET 6 D 7 ASN B 19 ASN B 30 -1 N TYR B 24 O ASN B 138 SHEET 7 D 7 ILE B 164 SER B 165 -1 O ILE B 164 N TYR B 28 SSBOND 1 CYS A 2 CYS A 122 1555 1555 2.00 SSBOND 2 CYS A 41 CYS A 171 1555 1555 2.06 SSBOND 3 CYS B 2 CYS B 122 1555 1555 1.99 SSBOND 4 CYS B 41 CYS B 171 1555 1555 2.03 LINK NE2 HIS A 59 FE AHEM A 201 1555 1555 1.94 LINK NE2 HIS A 59 FE BHEM A 201 1555 1555 2.07 LINK FE BHEM A 201 N NH3 A 202 1555 1555 2.01 LINK FE AHEM A 201 N NH3 A 202 1555 1555 2.14 LINK NE2 HIS B 59 FE BHEM B 201 1555 1555 1.98 LINK NE2 HIS B 59 FE AHEM B 201 1555 1555 2.03 LINK FE AHEM B 201 N NH3 B 202 1555 1555 1.99 LINK FE BHEM B 201 N NH3 B 202 1555 1555 2.04 SITE 1 AC1 22 VAL A 25 TYR A 28 VAL A 36 TYR A 40 SITE 2 AC1 22 ALA A 42 LEU A 44 LEU A 57 HIS A 59 SITE 3 AC1 22 PHE A 68 ASP A 70 PHE A 86 LYS A 88 SITE 4 AC1 22 TYR A 105 PHE A 107 LEU A 123 LYS A 125 SITE 5 AC1 22 LEU A 133 NH3 A 202 HOH A 346 HOH A 416 SITE 6 AC1 22 HOH A 429 HOH A 520 SITE 1 AC2 1 HEM A 201 SITE 1 AC3 6 PRO A 37 LYS A 38 ARG A 39 LYS A 63 SITE 2 AC3 6 HOH A 348 HOH A 374 SITE 1 AC4 23 VAL B 25 TYR B 28 VAL B 36 PRO B 37 SITE 2 AC4 23 TYR B 40 ALA B 42 LEU B 57 HIS B 59 SITE 3 AC4 23 PHE B 68 ASP B 70 PHE B 86 LYS B 88 SITE 4 AC4 23 TYR B 105 PHE B 107 ILE B 119 LEU B 123 SITE 5 AC4 23 LYS B 125 LEU B 130 LEU B 133 ALA B 135 SITE 6 AC4 23 NH3 B 202 HOH B 352 HOH B 473 SITE 1 AC5 1 HEM B 201 SITE 1 AC6 8 ALA A 1 GLN A 32 HOH A 403 HOH A 445 SITE 2 AC6 8 ALA B 145 LYS B 150 HOH B 394 HOH B 396 CRYST1 69.740 69.740 141.676 90.00 90.00 120.00 P 31 2 1 12 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 0.014339 0.008279 0.000000 0.00000 SCALE2 0.000000 0.016557 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007058 0.00000