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- PDB-1u17: 1.7 A Crystal structure of H60C mutant of Nitrophorin I. Heme com... -

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Basic information

Entry
Database: PDB / ID: 1u17
Title1.7 A Crystal structure of H60C mutant of Nitrophorin I. Heme complexed with two molecules imidazole
ComponentsNitrophorin 1
KeywordsSIGNALING PROTEIN / Lipocalin / beta barrel / heme / imidazole / bis-imidazole heme
Function / homology
Function and homology information


histamine binding / nitric oxide binding / vasodilation / extracellular region / metal ion binding
Similarity search - Function
Nitrophorin / Nitrophorin domain / Nitrophorin / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / PHOSPHATE ION / Nitrophorin-1
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVetter, S.W. / Goodin, D.B.
CitationJournal: TO BE PUBLISHED
Title: 1.7 A Crystal structure of H60C mutant of Nitrophorin I. Heme complexed with two molecules imidazole
Authors: Vetter, S.W. / Goodin, D.B.
History
DepositionJul 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitrophorin 1
B: Nitrophorin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,91310
Polymers41,2142
Non-polymers1,6998
Water5,585310
1
A: Nitrophorin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4575
Polymers20,6071
Non-polymers8504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nitrophorin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4575
Polymers20,6071
Non-polymers8504
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.006, 73.987, 65.224
Angle α, β, γ (deg.)90.00, 99.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nitrophorin 1 / NP1


Mass: 20607.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: pET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q26239
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M potassium cacodylate pH 5.3, 2.9 M di-ammoium hydrogen phospate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 24, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 40082 / % possible obs: 99.5 % / Redundancy: 3.9 % / Biso Wilson estimate: 20.3 Å2 / Rsym value: 0.074 / Net I/σ(I): 8.1
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1 / Rsym value: 0.33 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 2NP1

2np1


Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.028 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23713 1945 5 %RANDOM
Rwork0.18191 ---
all0.18469 ---
obs0.18469 36923 96.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.646 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å2-1.6 Å2
2--0.27 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2894 0 116 310 3320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223080
X-RAY DIFFRACTIONr_angle_refined_deg1.9622.0574186
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35368
X-RAY DIFFRACTIONr_chiral_restr0.1730.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022326
X-RAY DIFFRACTIONr_nbd_refined0.2270.21336
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2278
X-RAY DIFFRACTIONr_metal_ion_refined0.0660.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.233
X-RAY DIFFRACTIONr_mcbond_it1.3131.51836
X-RAY DIFFRACTIONr_mcangle_it2.33422942
X-RAY DIFFRACTIONr_scbond_it3.32431244
X-RAY DIFFRACTIONr_scangle_it5.2484.51244
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.377 128
Rwork0.312 2527

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