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- PDB-1eqd: CRYSTAL STRUCTURE OF NITROPHORIN 4 COMPLEXED WITH CN -

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Basic information

Entry
Database: PDB / ID: 1eqd
TitleCRYSTAL STRUCTURE OF NITROPHORIN 4 COMPLEXED WITH CN
ComponentsNITROPHORIN 4
KeywordsSIGNALING PROTEIN / beta barrel / lipocalin fold / ferric heme / cyanide
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 / CYANIDE ION / Chem-HEV / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / Resolution: 1.6 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: Nat.Struct.Biol. / Year: 1998
Title: Crystal structure of a nitric oxide transport protein from a blood-sucking insect.
Authors: Weichsel, A. / Andresen, J.F. / Champagne, D.E. / Walker, F.A. / Montfort, W.R.
History
DepositionApr 3, 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
Revision 1.6Nov 20, 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_sheet / 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_sheet.number_strands / _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

Downloads & links

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Assembly

Deposited unit
A: NITROPHORIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1514
Polymers20,2931
Non-polymers8593
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.036, 42.652, 52.559
Angle α, β, γ (deg.)90.00, 94.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-198-

HOH

21A-333-

HOH

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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-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#3: 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
#4: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 18.015 Da / Num. of mol.: 200 / 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: 36.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Oct 21, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→11 Å / Num. all: 32484 / Num. obs: 31409 / % possible obs: 87 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.65 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.5
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.16 / % possible all: 76
Reflection
*PLUS
Num. obs: 19393 / Num. measured all: 31409
Reflection shell
*PLUS
% possible obs: 76 % / Mean I/σ(I) obs: 3.5

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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: 1.6→11 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.26 926 random
Rwork0.2 --
all0.2 19393 -
obs0.2 18061 -
Refinement stepCycle: LAST / Resolution: 1.6→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 60 200 1688
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.035
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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