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- PDB-1d3s: 1.4 A crystal structure of nitrophorin 4 from Rhodnius prolixis a... -

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Basic information

Entry
Database: PDB / ID: 1d3s
Title1.4 A crystal structure of nitrophorin 4 from Rhodnius prolixis at pH=5.6.
ComponentsNITROPHORIN 4
KeywordsTRANSPORT PROTEIN / NITRIC OXIDE TRANSPORT / FERRIC HEME / ANTIHISTAMINE / VASODILATOR / LIPOCALIN
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 / Resolution: 1.4 Å
AuthorsWeichsel, A. / Andersen, J.F. / Roberts, S.A. / Montfort, W.R.
CitationJournal: 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.
History
DepositionSep 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 29, 2014Group: Other
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.6Oct 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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)20,9092
Polymers20,2931
Non-polymers6161
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.180, 42.520, 52.860
Angle α, β, γ (deg.)90.00, 94.35, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-206-

HOH

21A-207-

HOH

31A-208-

HOH

41A-290-

HOH

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Components

#1: Protein NITROPHORIN 4


Mass: 20292.664 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Description: SALIVARY GLAND / Plasmid: PET17B-NP4 / Species (production host): Escherichia coli / Organ (production host): SALIVARY GLAND / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / 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.: 197 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsAMMONIA (NH3) OCCUPIES THE FE SIXTH COORDINATION POSITION. THE HEME IS DISORDERED BY A ROTATION OF ...AMMONIA (NH3) OCCUPIES THE FE SIXTH COORDINATION POSITION. THE HEME IS DISORDERED BY A ROTATION OF 180 DEGREES AROUND THE CHA-FE-CHC AXIS. THE ONLY EVIDENCE OF THIS DISORDER IS THE APPEARENCE OF METHYL GROUPS CMB AND CMC AS VINYLS. THESE EXTRA ATOMS ARE CALLED CBBB AND CBCB. THE LOOP CONTAINING RESIDUES 32-38 IS DISORDERED. THERE IS NO OBSERVED ELECTRON DENSITY FOR THESE RESIDUES AND THEIR POSITIONS AND CONFORMATIONS ARE NOT RELIABLE.

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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: 36.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 23% PEG 4000 20 MM SODIUM CITRATE PH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
210 mMTris-HCl1drop
325 %(w/v)PEG40001reservoir
4100 mMsodium citrate1reservoir

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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: May 6, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 25227 / Num. obs: 25227 / % possible obs: 80 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.65 % / Biso Wilson estimate: 11.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.3
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.15 / % possible all: 79
Reflection
*PLUS
Num. measured all: 66833
Reflection shell
*PLUS
% possible obs: 79 %

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Processing

Software
NameVersionClassification
MADNESSdata collection
SCALAdata scaling
SHELXL-97refinement
MADNESSdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.4→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH-HUBER
Details: SHELXL REFINEMENT, FE, S ATOMS ANISOTROPIC (EXCEPT FOR C41SG WHICH IS DISORDERED) FE-LIGAND DISTANCES/ANGLES NOT RESTRAINED.
RfactorNum. reflectionSelection details
Rfree0.25 1284 RANDOM
Rwork0.21 --
all0.21 25227 -
obs0.21 25227 -
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 43 197 1668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.2 / Rfactor obs: 0.2 / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS

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