[English] 日本語
Yorodumi
- PDB-3ocz: Structure of Recombinant Haemophilus influenzae e(P4) Acid Phosph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ocz
TitleStructure of Recombinant Haemophilus influenzae e(P4) Acid Phosphatase Complexed with the inhibitor adenosine 5-O-thiomonophosphate
ComponentsLipoprotein E
KeywordsHydrolase/Hydrolase Inhibitor / hydrolase / outer membrane / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
5-nucleotidase lipoprotein e(P4) / Acid phosphatase, class B-like / HAD superfamily, subfamily IIIB (Acid phosphatase) / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE -5'-THIO-MONOPHOSPHATE / Lipoprotein E
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSingh, H. / Schuermann, J. / Reilly, T. / Calcutt, M. / Tanner, J.
CitationJournal: Febs J. / Year: 2011
Title: Structural basis of the inhibition of class C acid phosphatases by adenosine 5'-phosphorothioate.
Authors: Singh, H. / Reilly, T.J. / Tanner, J.J.
History
DepositionAug 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references
Revision 1.2Jan 11, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Sep 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipoprotein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0093
Polymers29,6211
Non-polymers3882
Water5,495305
1
A: Lipoprotein E
hetero molecules

A: Lipoprotein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0176
Polymers59,2422
Non-polymers7754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area8390 Å2
ΔGint-62 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.179, 98.179, 107.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-272-

HOH

21A-565-

HOH

31A-566-

HOH

-
Components

#1: Protein Lipoprotein E / Outer membrane protein P4 / OMP P4


Mass: 29620.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: periplasmic / Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: hel, HI_0693, ompP4 / Plasmid: pEt20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P26093, acid phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SRA / ADENOSINE -5'-THIO-MONOPHOSPHATE


Type: RNA linking / Mass: 363.287 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6PS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsG30E SEQUENCE CONFLICT IN UNP ENTRY P26093

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 18-23 % (w/v) PEG 3350, 0.05-0.2 M ammonium citrate dibasic, 0.05-0.15 mM MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 67160 / % possible obs: 100 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.072 / Χ2: 1.109 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.35-1.47.90.60766030.905199.9
1.4-1.4580.47865990.9021100
1.45-1.528.10.33666160.9241100
1.52-1.68.20.26266290.9441100
1.6-1.78.30.18666540.9841100
1.7-1.838.30.13666511.0331100
1.83-2.028.30.167151.2541100
2.02-2.318.30.08467381.81100
2.31-2.918.10.05268241.3461100
2.91-5080.0371310.973199.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3et4

3et4


Resolution: 1.35→33.286 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9294 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1585 3454 5.15 %
Rwork0.1381 --
obs0.1391 67093 99.93 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.145 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso max: 52.74 Å2 / Biso mean: 14.7201 Å2 / Biso min: 5.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.5597 Å2-0 Å20 Å2
2---1.5597 Å2-0 Å2
3---3.1194 Å2
Refinement stepCycle: LAST / Resolution: 1.35→33.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 24 305 2243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062009
X-RAY DIFFRACTIONf_angle_d1.0812725
X-RAY DIFFRACTIONf_chiral_restr0.08275
X-RAY DIFFRACTIONf_plane_restr0.005359
X-RAY DIFFRACTIONf_dihedral_angle_d13.41736
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.35-1.36790.25211530.22182469262299
1.3679-1.38740.22411270.193624992626100
1.3874-1.40820.20411390.172925112650100
1.4082-1.43020.18191340.153524872621100
1.4302-1.45360.17961490.141825212670100
1.4536-1.47870.16521410.127724972638100
1.4787-1.50560.16821390.121525062645100
1.5056-1.53450.17671300.116125302660100
1.5345-1.56580.16311290.112825002629100
1.5658-1.59990.14851400.104125282668100
1.5999-1.63710.1391380.096525242662100
1.6371-1.6780.12581250.101425152640100
1.678-1.72340.14071380.099525362674100
1.7234-1.77410.12761620.102725082670100
1.7741-1.83140.13991260.107525252651100
1.8314-1.89680.1391440.109825512695100
1.8968-1.97280.14461570.120125012658100
1.9728-2.06250.15071400.127125472687100
2.0625-2.17130.15261290.132925752704100
2.1713-2.30730.15351240.130625782702100
2.3073-2.48540.15191350.133625752710100
2.4854-2.73540.14541370.151526022739100
2.7354-3.13090.16071240.162926112735100
3.1309-3.94360.17041620.15226332795100
3.9436-33.29640.16611320.16162810294299

+
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