[English] 日本語
Yorodumi
- PDB-2at3: 1.00 A Crystal Structure Of L123V/L133V Mutant of Nitrophorin 4 F... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2at3
Title1.00 A Crystal Structure Of L123V/L133V Mutant of Nitrophorin 4 From Rhodnius Prolixus Complexed With Imidazole at pH 5.6
ComponentsNitrophorin 4
KeywordsTRANSPORT PROTEIN / Lipocalin / beta barrel / ferric heme / imidazole
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 / IMIDAZOLE / Nitrophorin-4
Similarity search - Component
Biological speciesRhodnius prolixus (insect)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1 Å
AuthorsAmoia, A.M. / Montfort, W.R.
CitationJournal: To be Published
Title: Heme distortion in nitrophorin 4: high resolution structures of mutated positions L123V and L133V and heme altered proteins
Authors: Amoia, A.M. / Montfort, W.R.
History
DepositionAug 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2006Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: Nitrophorin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9503
Polymers20,2651
Non-polymers6862
Water4,684260
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.221, 42.743, 52.886
Angle α, β, γ (deg.)90.00, 94.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-242-

HOH

21X-314-

HOH

31X-339-

HOH

41X-420-

HOH

DetailsThe biological assembly is a monomer consisting of chain X and the heme, and can be generated by the identity operation: x,y,z

-
Components

#1: Protein Nitrophorin 4 / NP4


Mass: 20264.609 Da / Num. of mol.: 1 / Mutation: L123V, L133V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodnius prolixus (insect) / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / 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: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.53 Å3/Da / Density % sol: 19.06 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium phosphate, imidazole, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 300.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.751 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 20, 2002 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: single crystal Si(311) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.751 Å / Relative weight: 1
ReflectionResolution: 1→19.81 Å / Num. obs: 81947 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.23 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.04 / Rsym value: 0.04 / Net I/σ(I): 20.8 / Scaling rejects: 2122
Reflection shellResolution: 1→1.04 Å / % possible obs: 88.1 % / Redundancy: 1.52 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.6 / Num. measured obs: 3534 / Num. unique all: 7330 / Rsym value: 0.25 / % possible all: 88

-
Processing

Software
NameVersionClassificationNB
d*TREK7.2SSIbetadata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
Blu-Icedata collection
CrystalClearV. 1.0 D*TREK (MSC/RIGAKU)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1X8O

1x8o


Resolution: 1→19.81 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.748 / SU ML: 0.018
Isotropic thermal model: anisotropic; residues 126-130 isotropic due to lack of density
Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / ESU R: 0.028 / ESU R Free: 0.028 / Stereochemistry target values: Engh & Huber
Details: Anisotropic refinement reduced Free R. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.167 4145 5.1 %RANDOM
Rwork0.144 ---
all0.145 81937 --
obs0.145 81937 97.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.376 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0.16 Å2
2--0.13 Å20 Å2
3----0.28 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å / Luzzati d res low obs: 4 Å
Refinement stepCycle: LAST / Resolution: 1→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1798 0 48 276 2122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221922
X-RAY DIFFRACTIONr_bond_other_d0.0020.021595
X-RAY DIFFRACTIONr_angle_refined_deg1.6582.0172662
X-RAY DIFFRACTIONr_angle_other_deg0.88933766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3815256
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9528.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35515316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.792153
X-RAY DIFFRACTIONr_chiral_restr0.0950.2274
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022299
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02387
X-RAY DIFFRACTIONr_nbd_refined0.4890.2469
X-RAY DIFFRACTIONr_nbd_other0.2350.21723
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2863
X-RAY DIFFRACTIONr_nbtor_other0.0880.21054
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2192
X-RAY DIFFRACTIONr_metal_ion_refined0.0140.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2110.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.232
X-RAY DIFFRACTIONr_mcbond_it1.5411.51479
X-RAY DIFFRACTIONr_mcbond_other1.0311.5470
X-RAY DIFFRACTIONr_mcangle_it1.89621909
X-RAY DIFFRACTIONr_scbond_it2.5843925
X-RAY DIFFRACTIONr_scangle_it3.1874.5739
X-RAY DIFFRACTIONr_rigid_bond_restr1.59632317
X-RAY DIFFRACTIONr_sphericity_free7.0353259
X-RAY DIFFRACTIONr_sphericity_bonded3.53231772
LS refinement shellResolution: 1.001→1.027 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 261 -
Rwork0.247 5002 -
all-5263 -
obs--85.52 %

+
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://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