[English] 日本語
Yorodumi
- PDB-4np1: NITROPHORIN 1 COMPLEX WITH NITRIC OXIDE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4np1
TitleNITROPHORIN 1 COMPLEX WITH NITRIC OXIDE
ComponentsNITROPHORIN 1
KeywordsVASODILATOR / NITRIC OXIDE TRANSPORT / HEME / ANTIHISTAMINE / LIPOCALIN
Function / homology
Function and homology information


histamine binding / nitric oxide binding / vasodilation / 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 / NITRIC OXIDE / PHOSPHATE ION / Nitrophorin-1
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 2.3 Å
AuthorsWeichsel, A. / Andersen, J.F. / Walker, F.A. / Montfort, W.R.
Citation
Journal: To be Published
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.Kh. / Balfour, C. / Pierik, A. / Averill, B.A. / Montfort, W.R. / Walker, F.A.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Crystal Structures of a Nitric Oxide Transport Protein from a Blood-Sucking Insect
Authors: Weichsel, A. / Andersen, J.F. / Champagne, D.E. / Walker, F.A. / Montfort, W.R.
#2: Journal: Biochemistry / Year: 1997
Title: Nitric Oxide Binding and Crystallization of Recombinant Nitrophorin I, a Nitric Oxide Transport Protein from the Blood-Sucking Bug Rhodnius Prolixus
Authors: Andersen, J.F. / Champagne, D.E. / Weichsel, A. / Ribeiro, J.M. / Balfour, C.A. / Dress, V. / Montfort, W.R.
History
DepositionJun 26, 1998Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Refinement description / Category: diffrn_detector / pdbx_database_status / software
Item: _diffrn_detector.detector / _pdbx_database_status.process_site / _software.name
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NITROPHORIN 1
B: NITROPHORIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,69510
Polymers41,0222
Non-polymers1,6738
Water2,540141
1
A: NITROPHORIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3475
Polymers20,5111
Non-polymers8364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NITROPHORIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3475
Polymers20,5111
Non-polymers8364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.410, 74.290, 66.120
Angle α, β, γ (deg.)90.00, 99.19, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.686192, -0.040491, -0.726292), (-0.057147, -0.998364, 0.001667), (-0.725172, 0.040362, -0.687384)
Vector: 43.1843, 76.9003, 97.4409)

-
Components

#1: Protein NITROPHORIN 1 / NP1


Mass: 20510.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Cell line: BL21 / Organ: SALIVARY GLAND / Plasmid: PET17B-NP1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q26239
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.5
Details: 2.8 M AMMONIUM PHOSPHATE, 0.1 M TRIS.HCL, PH 7.5, ROOM TEMPERATURE

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Nov 17, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→28 Å / Num. obs: 18071 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 28 Å2 / Rsym value: 0.058 / Net I/σ(I): 9.2
Reflection shellResolution: 2.2→2.35 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.258 / % possible all: 87.7

-
Processing

Software
NameVersionClassification
MADNESdata collection
AGROVATA/ROTAVATAdata reduction
X-PLOR3.851model building
X-PLOR3.851refinement
MADNESdata reduction
Agrovatadata scaling
ROTAVATAdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1NP1

1np1


Resolution: 2.3→15 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1000000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3 354 5 %RANDOM
Rwork0.19 ---
obs0.19 13528 84.7 %-
Displacement parametersBiso mean: 36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-15 Å
Luzzati sigma a0.26 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 100 141 3127
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d30.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.18
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.71.5
X-RAY DIFFRACTIONx_mcangle_it4.52
X-RAY DIFFRACTIONx_scbond_it3.82
X-RAY DIFFRACTIONx_scangle_it5.82.5
Refine LS restraints NCSNCS model details: UNRESTRAINED
LS refinement shellResolution: 2.3→2.4 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.28 22 5 %
Rwork0.29 1100 -
obs--58 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19X.HEME
X-RAY DIFFRACTION3PARAM.PO4TOP.PO4
X-RAY DIFFRACTION4PARAM19.SOLTOPH19.SOL

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more