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- PDB-1x8q: 0.85 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus ... -

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Basic information

Entry
Database: PDB / ID: 1x8q
Title0.85 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus in Complex with Water at pH 5.6
ComponentsNitrophorin 4
KeywordsLIGAND BINDING PROTEIN / Lipocalin / beta barrel / ferric heme
Function / homology
Function and homology information


nitrite dismutase / histamine binding / nitric oxide binding / vasodilation / oxidoreductase activity / 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 / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.85 Å
AuthorsKondrashov, D.A. / Roberts, S.A. / Weichsel, A. / Montfort, W.R.
CitationJournal: Biochemistry / Year: 2004
Title: Protein functional cycle viewed at atomic resolution: conformational change and mobility in nitrophorin 4 as a function of pH and NO binding
Authors: Kondrashov, D.A. / Roberts, S.A. / Weichsel, A. / Montfort, W.R.
History
DepositionAug 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 17, 2014Group: Non-polymer description
Revision 1.4Aug 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nitrophorin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9092
Polymers20,2931
Non-polymers6161
Water6,485360
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.323, 42.486, 53.018
Angle α, β, γ (deg.)90.00, 94.45, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-308-

HOH

21A-390-

HOH

31A-498-

HOH

41A-539-

HOH

DetailsThe biological assembly is a monomer consisting of chain A and the heme, and can be generated by the identity operation: x,y,z

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Components

#1: Protein Nitrophorin 4 / NP4


Mass: 20292.664 Da / Num. of mol.: 1
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): BL21DE3 / References: UniProt: Q94734
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.63 Å3/Da / Density % sol: 24.3 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 24, 2002 / Details: Bent conical Si-mirror (Rh coating)
RadiationMonochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 0.85→22 Å / Num. all: 113651 / Num. obs: 113651 / % possible obs: 80.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 8 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 19.4
Reflection shellResolution: 0.85→0.88 Å / Redundancy: 3 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.4 / Num. unique all: 8407 / Rsym value: 0.23 / % possible all: 63.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
d*TREK(Crystal Clear)data reduction
SHELXmodel building
SHELXL-97refinement
CrystalClearD*TREK (MSC/RIGAKU)data scaling
SHELXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1D2U

1d2u


Resolution: 0.85→6 Å / Num. parameters: 18103 / Num. restraintsaints: 19193 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 3.9%. Hydrogens were added in calculated positions, further reducing free R by 1%.
RfactorNum. reflection% reflectionSelection details
Rfree0.1303 5578 5 %RANDOM
Rwork0.1037 ---
all0.1051 110585 --
obs0.10371 110585 81.2 %-
Displacement parametersBiso mean: 12.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.097 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 103 / Occupancy sum hydrogen: 1394.2 / Occupancy sum non hydrogen: 1802.79
Refinement stepCycle: LAST / Resolution: 0.85→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 43 360 1831
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.037
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.462
X-RAY DIFFRACTIONs_zero_chiral_vol0.086
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.116
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.115
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.066
X-RAY DIFFRACTIONs_approx_iso_adps0.126

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