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- PDB-1ywd: 1.08 A Structure of Ferrous NP4 (aquo complex) -

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Basic information

Entry
Database: PDB / ID: 1ywd
Title1.08 A Structure of Ferrous NP4 (aquo complex)
Componentsnitrophorin 4
KeywordsLIGAND BINDING PROTEIN / BLOOD CLOTTING / ferrous heme / lipocalin fold / beta barrel
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 / starting model 1D2U / Resolution: 1.08 Å
AuthorsMaes, E.M. / Weichsel, A. / Roberts, S.A. / Montfort, W.R.
CitationJournal: Biochemistry / Year: 2005
Title: Ultrahigh Resolution Structures of Nitrophorin 4: Heme Distortion in Ferrous CO and NO Complexes
Authors: Maes, E.M. / Roberts, S.A. / Weichsel, A. / Montfort, W.R.
History
DepositionFeb 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 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 / 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 6, 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
Water5,368298
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.063, 42.905, 52.272
Angle α, β, γ (deg.)90.00, 94.37, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-274-

HOH

21A-414-

HOH

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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.: 298 / 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: 1.93 Å3/Da / Density % sol: 36.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 2.8 M ammonium phosphate, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.751 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 20, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.751 Å / Relative weight: 1
ReflectionResolution: 1.08→30 Å / Num. all: 64299 / Num. obs: 64299 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rsym value: 0.052 / Net I/σ(I): 9.1
Reflection shellResolution: 1.08→1.12 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2 / Num. unique all: 6266 / Rsym value: 0.228 / % possible all: 99

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Processing

Software
NameClassification
d*TREKdata reduction
SHELXL-97refinement
d*TREKdata scaling
RefinementMethod to determine structure: starting model 1D2U
Starting model: PDB ID 1D2U

1d2u


Resolution: 1.08→10 Å
Isotropic thermal model: individual anisotropic thermal parameters
Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.17 3221 -random
Rwork0.14 ---
all0.141 64231 --
obs0.141 64231 99 %-
Refinement stepCycle: LAST / Resolution: 1.08→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1481 0 43 300 1824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.035

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