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- PDB-1x8n: 1.08 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus ... -

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Basic information

Entry
Database: PDB / ID: 1x8n
Title1.08 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Complexed With Nitric Oxide at pH 7.4
ComponentsNitrophorin 4
KeywordsLIGAND BINDING PROTEIN / Lipocalin / beta barrel / heme / nitric oxide
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 / NITRIC OXIDE / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.08 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 1.3Aug 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 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)20,9393
Polymers20,2931
Non-polymers6462
Water5,693316
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.147, 42.775, 53.042
Angle α, β, γ (deg.)90.00, 94.09, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-275-

HOH

21A-368-

HOH

31A-387-

HOH

41A-394-

HOH

51A-447-

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: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 24.7 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: ammonium phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 16, 2002 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.08→36 Å / Num. all: 66157 / Num. obs: 66157 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 10.7 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 10.4
Reflection shellResolution: 1.08→1.12 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 1.8 / Num. unique all: 6226 / Rsym value: 0.27 / % possible all: 95.1

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Processing

Software
NameVersionClassification
DENZOdata 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: 1KOI

1koi


Resolution: 1.08→6 Å / Num. parameters: 16428 / Num. restraintsaints: 15840
Isotropic thermal model: anisotropic, except for residues 32-26 and 126-130
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 2.6%. Addition of hydrogens in calculated positions further reduced free R by 1.3%
RfactorNum. reflection% reflectionSelection details
Rfree0.1714 3303 5 %RANDOM
Rwork0.1341 ---
all0.136 65756 --
obs0.13411 65756 98.4 %-
Displacement parametersBiso mean: 14.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.133 Å / Luzzati d res low obs: 5 Å / Num. disordered residues: 60 / Occupancy sum hydrogen: 1341 / Occupancy sum non hydrogen: 1766.55
Refinement stepCycle: LAST / Resolution: 1.08→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1552 0 45 316 1913
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.426
X-RAY DIFFRACTIONs_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.032
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.051
X-RAY DIFFRACTIONs_approx_iso_adps0.087

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