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- PDB-1euo: Crystal structure of nitrophorin 2 (prolixin-S) -

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Basic information

Entry
Database: PDB / ID: 1euo
TitleCrystal structure of nitrophorin 2 (prolixin-S)
ComponentsNITROPHORIN 2
KeywordsSIGNALING PROTEIN / beta barrel / lipocalin / heme
Function / homology
Function and homology information


histamine binding / nitric oxide binding / vasodilation / toxin 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 / AMMONIA / Nitrophorin-2
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsAndersen, J.F. / Montfort, W.R.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The crystal structure of nitrophorin 2. A trifunctional antihemostatic protein from the saliva of Rhodnius prolixus
Authors: Andersen, J.F. / Montfort, W.R.
History
DepositionApr 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _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.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_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

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Assembly

Deposited unit
A: NITROPHORIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7143
Polymers20,0801
Non-polymers6342
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.340, 127.960, 33.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-259-

HOH

DetailsThe biological assembly is a monomer containing a single heme prosthetic group. His 57 forms the proximal heme ligand, and NH3 forms the distal ligand.

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Components

#1: Protein NITROPHORIN 2 / PROLIXIN-S


Mass: 20080.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Gene: SALIVARY GLAND CDNA / Organ: SALIVARY GLAND / Plasmid: PET 17B / Production host: Escherichia coli (E. coli) / References: UniProt: Q26241
#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-NH3 / AMMONIA


Mass: 17.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: ammonium phosphate, Tris-HCl, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.8 Mammonium phosphate1reservoir
20.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Oct 30, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→9.2 Å / Num. all: 12186 / Num. obs: 12186 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 4.5
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.35 / Num. unique all: 187 / % possible all: 90.3
Reflection
*PLUS
Num. measured all: 49410
Reflection shell
*PLUS
% possible obs: 90.3 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
MADNESSdata collection
SCALAdata scaling
X-PLORmodel building
CNSrefinement
MADNESSdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementResolution: 2→9.2 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: Used simulated annealing and maximum likelihood procedures.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 599 -Random
Rwork0.195 ---
all0.197 11592 --
obs0.197 11592 94.3 %-
Refinement stepCycle: LAST / Resolution: 2→9.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1411 0 44 80 1535
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.27
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.19 / Rfactor obs: 0.19 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.006

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