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- PDB-1erx: CRYSTAL STRUCTURE OF NITROPHORIN 4 COMPLEXED WITH NO -

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Basic information

Entry
Database: PDB / ID: 1erx
TitleCRYSTAL STRUCTURE OF NITROPHORIN 4 COMPLEXED WITH NO
ComponentsNITROPHORIN 4
KeywordsSIGNALING PROTEIN / beta barrel / ferric heme / nitric oxide complex
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
CITRIC ACID / Chem-HEV / NITRIC OXIDE / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsWeichsel, A. / Andersen, J.F. / Roberts, S.A. / Montfort, W.R.
Citation
Journal: Nat.Struct.Biol. / Year: 2000
Title: Nitric oxide binding to nitrophorin 4 induces complete distal pocket burial.
Authors: Weichsel, A. / Andersen, J.F. / Roberts, S.A. / Montfort, W.R.
#1: Journal: Structure / Year: 1998
Title: The crystal structure of nitrophorin 4 at 1.5 A resolution: transport of nitric oxide by a lipocalin-based heme protein.
Authors: Andersen, J.F. / Weichsel, A. / Balfour, C.A. / Champagne, D.E. / Montfort, W.R.
#2: Journal: J.Am.Chem.Soc. / Year: 1999
Title: Nitric oxide binding to the ferri- and ferroheme states of nitrophorin 1, a reversible NO-binding heme protein from the saliva of the blood-sucking insect, rhodnius prolixus.
Authors: Ding, X.D. / Weichsel, A. / Andersen, J.F. / Shokhireva, T.K. / Balfour, C.A. / Pierik, A.J. / Averill, B.A. / Montfort, W.R. / Walker, F.A.
History
DepositionApr 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 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 1.4Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector

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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)21,1554
Polymers20,2931
Non-polymers8633
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.319, 42.636, 52.573
Angle α, β, γ (deg.)90.00, 94.19, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-273-

HOH

21A-338-

HOH

Detailsbiological assembly is a monomer

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Components

#1: Protein NITROPHORIN 4 /


Mass: 20292.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SALIVA / Source: (natural) Rhodnius prolixus (insect) / References: UniProt: Q94734
#2: Chemical ChemComp-HEV / 5,8-DIMETHYL-1,2,3,4-TETRAVINYLPORPHINE-6,7-DIPROPIONIC ACID FERROUS COMPLEX / 1,3-DEDIMETHYL-1,3-DIVINYL HEME


Mass: 640.509 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C36H32FeN4O4
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 1.94 Å3/Da / Density % sol: 36.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Details: drop consists of 1:1 mixture of well and protein solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
210 mMTris-HCl1drop
350 %(w/v)PEG40001reservoir
4100 mMsodium citrate1reservoir
5argon1reservoir

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Apr 29, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→15 Å / Num. all: 28023 / Num. obs: 28023 / % possible obs: 91 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.9
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.3 / Num. unique all: 3546 / % possible all: 79
Reflection
*PLUS
Num. measured all: 56842
Reflection shell
*PLUS
% possible obs: 79 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
MADNESSdata collection
SCALAdata scaling
X-PLORmodel building
SHELXL-97refinement
MADNESSdata reduction
CCP4(SCALA)data scaling
X-PLORphasing
RefinementResolution: 1.4→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: anisotropic temperature factor refinement
RfactorNum. reflectionSelection details
Rfree0.24 1401 random
Rwork0.17 --
all0.17 28023 -
obs0.17 26521 -
Refinement stepCycle: LAST / Resolution: 1.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1436 0 62 160 1658
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.039

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