[English] 日本語
Yorodumi
- PDB-5gne: Crystal structure of LapB from Legionella pneumophila -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gne
TitleCrystal structure of LapB from Legionella pneumophila
ComponentsLeucine aminopeptidaseLeucyl aminopeptidase
KeywordsHYDROLASE / Aminopeptidase / Legionella pneumophila / PA domain / autoinhibition
Function / homologymetalloexopeptidase activity / Peptidase M28 / Peptidase family M28 / aminopeptidase activity / Leucine aminopeptidase
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZhang, N. / Ge, H.
Funding support China, 2items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31270770 China
the National Natural Science Foundation of China31400641 China
CitationJournal: J. Agric. Food Chem. / Year: 2017
Title: Crystal Structure and Biochemical Characterization of an Aminopeptidase LapB from Legionella pneumophila.
Authors: Zhang, N. / Yin, S. / Zhang, W. / Gong, X. / Zhang, N. / Fang, K. / Ge, H.
History
DepositionJul 20, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 17, 2018Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_Rpim_I_all
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Leucine aminopeptidase
B: Leucine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,9608
Polymers84,5072
Non-polymers4546
Water82946
1
A: Leucine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4804
Polymers42,2531
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leucine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4804
Polymers42,2531
Non-polymers2273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)152.970, 152.970, 108.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
Components

#1: Protein Leucine aminopeptidase / Leucyl aminopeptidase


Mass: 42253.312 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 24-397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg0032 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q5ZZH8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.75 Å3/Da / Density % sol: 67.22 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M Sodium citrate tribasic dihydrate pH 6.0, 0.32 M Ammonium sulfate, 1.0 M Lithium sulfate monohydrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.5→48 Å / Num. obs: 42854 / % possible obs: 95.1 % / Redundancy: 17.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.04 / Net I/σ(I): 18.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 17.8 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 3 / Num. unique obs: 4641 / CC1/2: 0.837 / Rpim(I) all: 0.425 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
MOSFLMdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AMP

1amp


Resolution: 2.5→48 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.227 2121 4.96 %RANDOM
Rwork0.18 ---
obs0.1826 42787 95.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5838 0 14 46 5898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015982
X-RAY DIFFRACTIONf_angle_d1.418114
X-RAY DIFFRACTIONf_dihedral_angle_d15.3932186
X-RAY DIFFRACTIONf_chiral_restr0.066905
X-RAY DIFFRACTIONf_plane_restr0.0071048
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.55820.32021540.25552764X-RAY DIFFRACTION100
2.5582-2.62210.27881610.23522783X-RAY DIFFRACTION100
2.6221-2.6930.32581090.24481966X-RAY DIFFRACTION70
2.693-2.77230.28071330.22082828X-RAY DIFFRACTION100
2.7723-2.86170.2921640.22772785X-RAY DIFFRACTION100
2.8617-2.9640.24031350.21462838X-RAY DIFFRACTION100
2.964-3.08270.27991540.22012811X-RAY DIFFRACTION100
3.0827-3.22290.24841560.21042811X-RAY DIFFRACTION100
3.2229-3.39280.27851490.21562847X-RAY DIFFRACTION100
3.3928-3.60530.24361280.20122335X-RAY DIFFRACTION82
3.6053-3.88360.21191140.17752461X-RAY DIFFRACTION86
3.8836-4.27420.21781420.14922536X-RAY DIFFRACTION88
4.2742-4.89220.15871270.13542899X-RAY DIFFRACTION100
4.8922-6.16170.20191450.16052932X-RAY DIFFRACTION100
6.1617-48.46960.19331500.16033070X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.50460.27-0.892.02430.38272.5717-0.111-0.17260.21470.279-0.1637-0.05970.1370.14080.1430.26180.0351-0.01260.34140.06270.471310.7402-7.9143-23.6518
21.45670.43311.75550.85752.29856.3891-0.4059-0.05160.1292-0.9784-0.13290.0212-0.2499-0.0770.51030.37970.09650.15030.4138-0.01230.416-3.6216-23.8942-52.6111
31.82710.79751.07661.66131.54254.22430.0407-0.2833-0.0394-0.0352-0.2722-0.06690.2742-0.59390.14710.3028-0.02490.16290.29640.03220.4172-0.3983-26.2048-38.5621
43.6328-1.33050.23863.19820.18053.3482-0.02160.29210.1055-0.0816-0.0928-0.19010.33610.63420.06770.22990.15830.0290.7020.38090.526140.9079-13.1314-43.299
52.4708-1.5481.25742.3569-0.89551.2406-0.395-0.36590.21690.56630.3013-0.11870.03840.1587-0.04610.46250.1880.03330.77230.23430.545643.1586-21.8673-22.8524
62.1415-0.94180.3331.7513-0.36522.5975-0.2932-0.5531-0.24120.58820.50270.34250.0698-0.4607-0.2860.62740.54270.10411.11560.56540.548439.6922-29.5659-19.0555
72.68762.23561.06793.49051.10817.3903-0.30890.02050.6430.26220.0867-0.3758-0.72410.69790.20710.82640.2862-0.24070.96210.00530.704756.8681-18.0661-17.8075
83.41370.97132.22351.074-0.4315.2302-0.29290.17250.64730.21520.214-0.0313-0.74580.25740.1010.8040.3514-0.20820.80410.1020.680349.6512-16.0444-20.7077
91.2228-1.07362.4790.9922-2.04295.4031-0.21580.11480.44350.14910.1088-0.9027-0.47781.04310.13810.56060.2499-0.06261.04390.1210.634958.8152-27.8921-31.7305
104.2077-1.89460.89746.22170.00254.3431-0.4078-0.47870.3281.04890.4737-0.1895-0.3774-0.1991-0.04950.88240.5484-0.16510.94030.08040.492553.2418-25.5145-10.4218
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 104 )
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 397 )
4X-RAY DIFFRACTION4chain 'B' and (resid 28 through 77 )
5X-RAY DIFFRACTION5chain 'B' and (resid 78 through 153 )
6X-RAY DIFFRACTION6chain 'B' and (resid 154 through 286 )
7X-RAY DIFFRACTION7chain 'B' and (resid 287 through 322 )
8X-RAY DIFFRACTION8chain 'B' and (resid 323 through 356 )
9X-RAY DIFFRACTION9chain 'B' and (resid 357 through 376 )
10X-RAY DIFFRACTION10chain 'B' and (resid 377 through 397 )

+
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