HEADER TRANSPORT PROTEIN 24-AUG-05 2ASZ OBSLTE 04-MAR-08 2ASZ 3C76 TITLE 1.07 A CRYSTAL STRUCTURE OF L133V MUTANT OF NITROPHORIN 4 TITLE 2 FROM RHODNIUS PROLIXUS COMPLEXED WITH AMMONIA AT PH 7.5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITROPHORIN 4; COMPND 3 CHAIN: X; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21DE3; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS LIPOCALIN, BETA BARREL, FERRIC HEME EXPDTA X-RAY DIFFRACTION AUTHOR A.M.AMOIA,W.R.MONTFORT REVDAT 2 04-MAR-08 2ASZ 1 OBSLTE REVDAT 1 22-AUG-06 2ASZ 0 JRNL AUTH A.M.AMOIA,W.R.MONTFORT JRNL TITL HEME DISTORTION IN NITROPHORIN 4: HIGH RESOLUTION JRNL TITL 2 STRUCTURES OF MUTATED POSITIONS L123V AND L133V JRNL TITL 3 AND HEME ALTERED PROTEINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 67317 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.165 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3416 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH : 1.07 REMARK 3 BIN RESOLUTION RANGE LOW : 1.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4740 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.34 REMARK 3 BIN R VALUE (WORKING SET) : 0.1850 REMARK 3 BIN FREE R VALUE SET COUNT : 237 REMARK 3 BIN FREE R VALUE : 0.2160 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 ALL ATOMS : 2060 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.07000 REMARK 3 B22 (A**2) : -0.12000 REMARK 3 B33 (A**2) : 0.05000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.033 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.033 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.018 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.783 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1831 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1510 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2542 ; 1.743 ; 2.018 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3560 ; 0.889 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 242 ; 7.791 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 81 ;37.505 ;28.519 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 292 ;12.807 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ; 8.491 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 262 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2186 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 373 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 454 ; 0.417 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1645 ; 0.220 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 875 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1046 ; 0.091 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 203 ; 0.160 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.049 ; 0.200 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): 13 ; 0.085 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 48 ; 0.189 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 34 ; 0.100 ; 0.200 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): 1400 ; 1.836 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 445 ; 0.685 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1810 ; 2.235 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 896 ; 3.073 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 718 ; 3.716 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4070 ; 1.467 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 312 ; 7.658 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3265 ; 3.229 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 0 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 0 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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: ANISOTROPIC REFINMENT REDUCED FREE REMARK 3 R. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 2ASZ COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.101 (2007-05-29) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE RCSB ID CODE IS RCSB034277. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-2002 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE-CRYSTAL REMARK 200 OPTICS : BENT-FLAT SI-MIRROR (RH REMARK 200 COATING) REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR V. 1.0 D*TREK REMARK 200 (MSC/RIGAKU) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67479 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.070 REMARK 200 RESOLUTION RANGE LOW (A) : 19.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : 7.120 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : 0.06000 REMARK 200 FOR THE DATA SET : 15.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.79 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : 0.30000 REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1X8P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 23.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM PHOSPHATE, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 300.0K 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 35.16000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.42350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.16000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.42350 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: X 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 244 LIES ON A SPECIAL POSITION. REMARK 375 HOH 333 LIES ON A SPECIAL POSITION. REMARK 375 HOH 459 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASP X 34 ASP X 35 147.65 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AT0 RELATED DB: PDB REMARK 900 L133V MUTANT OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS REMARK 900 COMPLEXED WITH NITRIC OXIDE AT PH 5.6 REMARK 900 RELATED ID: 2AT3 RELATED DB: PDB REMARK 900 L123V/L133V MUTANT OF NITROPHORIN 4 FROM RHODNIUS PROLIXUS REMARK 900 COMPLEXED WITH IMIDAZOLE AT PH 5.6 REMARK 900 RELATED ID: 1X8P RELATED DB: PDB REMARK 900 NITROPHORIN 4 COMPLEXED WITH AMMONIA AT PH 7.4 DBREF 2ASZ X 1 184 UNP Q94734 NP4_RHOPR 22 205 SEQADV 2ASZ VAL X 133 UNP Q94734 LEU 154 ENGINEERED SEQRES 1 X 184 ALA CYS THR LYS ASN ALA ILE ALA GLN THR GLY PHE ASN SEQRES 2 X 184 LYS ASP LYS TYR PHE ASN GLY ASP VAL TRP TYR VAL THR SEQRES 3 X 184 ASP TYR LEU ASP LEU GLU PRO ASP ASP VAL PRO LYS ARG SEQRES 4 X 184 TYR CYS ALA ALA LEU ALA ALA GLY THR ALA SER GLY LYS SEQRES 5 X 184 LEU LYS GLU ALA LEU TYR HIS TYR ASP PRO LYS THR GLN SEQRES 6 X 184 ASP THR PHE TYR ASP VAL SER GLU LEU GLN VAL GLU SER SEQRES 7 X 184 LEU GLY LYS TYR THR ALA ASN PHE LYS LYS VAL ASP LYS SEQRES 8 X 184 ASN GLY ASN VAL LYS VAL ALA VAL THR ALA GLY ASN TYR SEQRES 9 X 184 TYR THR PHE THR VAL MET TYR ALA ASP ASP SER SER ALA SEQRES 10 X 184 LEU ILE HIS THR CYS LEU HIS LYS GLY ASN LYS ASP LEU SEQRES 11 X 184 GLY ASP VAL TYR ALA VAL LEU ASN ARG ASN LYS ASP ALA SEQRES 12 X 184 ALA ALA GLY ASP LYS VAL LYS SER ALA VAL SER ALA ALA SEQRES 13 X 184 THR LEU GLU PHE SER LYS PHE ILE SER THR LYS GLU ASN SEQRES 14 X 184 ASN CYS ALA TYR ASP ASN ASP SER LEU LYS SER LEU LEU SEQRES 15 X 184 THR LYS HET NH4 X 186 1 HET HEM X 185 43 HETNAM NH4 AMMONIUM ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 NH4 H4 N 1+ FORMUL 3 HEM C34 H32 FE N4 O4 FORMUL 4 HOH *296(H2 O) HELIX 1 1 ASN X 13 PHE X 18 1 6 HELIX 2 2 GLU X 32 VAL X 36 5 5 HELIX 3 3 GLY X 146 ALA X 156 1 11 HELIX 4 4 GLU X 159 PHE X 163 5 5 HELIX 5 5 ASP X 174 LEU X 182 1 9 SHEET 1 A 7 VAL X 95 VAL X 97 0 SHEET 2 A 7 LYS X 81 VAL X 89 -1 N LYS X 88 O LYS X 96 SHEET 3 A 7 THR X 67 SER X 78 -1 N GLU X 77 O LYS X 81 SHEET 4 A 7 LYS X 52 TYR X 60 -1 N LEU X 57 O ASP X 70 SHEET 5 A 7 CYS X 41 ALA X 49 -1 N GLY X 47 O LYS X 54 SHEET 6 A 7 ASN X 19 ASP X 30 -1 N TRP X 23 O LEU X 44 SHEET 7 A 7 ILE X 164 SER X 165 -1 O ILE X 164 N TYR X 28 SHEET 1 B 7 VAL X 95 VAL X 97 0 SHEET 2 B 7 LYS X 81 VAL X 89 -1 N LYS X 88 O LYS X 96 SHEET 3 B 7 TYR X 104 ALA X 112 -1 O TYR X 105 N ALA X 84 SHEET 4 B 7 SER X 116 HIS X 124 -1 O HIS X 124 N TYR X 104 SHEET 5 B 7 ASP X 132 ASN X 138 -1 O LEU X 137 N ALA X 117 SHEET 6 B 7 ASN X 19 ASP X 30 -1 N LEU X 29 O TYR X 134 SHEET 7 B 7 ILE X 164 SER X 165 -1 O ILE X 164 N TYR X 28 SSBOND 1 CYS X 2 CYS X 122 SSBOND 2 CYS X 41 CYS X 171 LINK NE2 HIS X 59 FE HEM X 185 LINK N NH4 X 186 FE HEM X 185 CRYST1 70.320 42.847 52.871 90.00 94.26 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 0.014220 0.000000 0.001060 0.00000 SCALE2 0.000000 0.023340 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018970 0.00000