[English] 日本語
Yorodumi
- PDB-3lnn: Crystal structure of ZneB from Cupriavidus metallidurans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lnn
TitleCrystal structure of ZneB from Cupriavidus metallidurans
ComponentsMembrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
KeywordsMETAL TRANSPORT / membrane fusion protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Structures of Membrane Proteins / CSMP / MEMBRANE PROTEIN
Function / homology
Function and homology information


cell envelope / transmembrane transporter activity / membrane / metal ion binding
Similarity search - Function
: / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Helix hairpin bin / Efflux pump adaptor protein, beta barrel domain / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion ...: / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold - #20 / conserved putative lor/sdh protein from methanococcus maripaludis s2 fold / Helix hairpin bin / Efflux pump adaptor protein, beta barrel domain / Cation efflux system protein CusB, domain 1 / Cation efflux system protein CusB domain 1 / RND efflux pump, membrane fusion protein / RND efflux pump, membrane fusion protein, barrel-sandwich domain / Barrel-sandwich domain of CusB or HlyD membrane-fusion / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Elongation Factor Tu (Ef-tu); domain 3 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Membrane fusion protein (MFP-RND) heavy metal cation tricomponent efflux HmxB (CzcB-like)
Similarity search - Component
Biological speciesCupriavidus metallidurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.796 Å
AuthorsLee, J.K. / De Angelis, F. / Miercke, L.J. / Stroud, R.M. / Vandenbussche, G. / Center for Structures of Membrane Proteins (CSMP)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Metal-induced conformational changes in ZneB suggest an active role of membrane fusion proteins in efflux resistance systems.
Authors: De Angelis, F. / Lee, J.K. / O'Connell, J.D. / Miercke, L.J. / Verschueren, K.H. / Srinivasan, V. / Bauvois, C. / Govaerts, C. / Robbins, R.A. / Ruysschaert, J.M. / Stroud, R.M. / Vandenbussche, G.
History
DepositionFeb 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
B: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6573
Polymers77,5922
Non-polymers651
Water28816
1
A: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8612
Polymers38,7961
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)


Theoretical massNumber of molelcules
Total (without water)38,7961
Polymers38,7961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
B: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
hetero molecules

A: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
B: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,3156
Polymers155,1844
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area9640 Å2
ΔGint-103 kcal/mol
Surface area57460 Å2
MethodPISA
4
A: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
B: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
hetero molecules

A: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
B: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
hetero molecules

A: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
B: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
hetero molecules

A: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
B: Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)310,62912
Polymers310,3688
Non-polymers2624
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area26470 Å2
ΔGint-235 kcal/mol
Surface area107740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.111, 137.111, 202.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

-
Components

#1: Protein Membrane fusion protein (MFP) heavy metal cation efflux ZneB (CzcB-like) / Secretion protein HlyD


Mass: 38795.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus metallidurans (bacteria) / Strain: CH34 / Gene: Rmet_5330, ZneB / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1LCD7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1M Na-Acetate pH 5.4 1.9M Na-formate 3% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.3.110.9796
SYNCHROTRONESRF ID23-121.0762
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDJun 28, 2009Double crystal Si(111)
ADSC QUANTUM 3152CCDMay 19, 2009Single Si(111)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Single crystal Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
21.07621
ReflectionResolution: 2.796→32.959 Å / Num. all: 23803 / Num. obs: 20621 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.5 % / Biso Wilson estimate: 72.76 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.074 / Net I/σ(I): 21
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 14 % / Mean I/σ(I) obs: 2.06 / Num. unique all: 2360 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.796→32.959 Å / SU ML: 0.48 / σ(F): 0.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3135 1058 5.13 %RANDOM
Rwork0.2374 ---
obs0.2413 20621 85.07 %-
all-23803 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.18 Å2 / ksol: 0.294 e/Å3
Refinement stepCycle: LAST / Resolution: 2.796→32.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4344 0 1 16 4361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014516
X-RAY DIFFRACTIONf_angle_d1.7386140
X-RAY DIFFRACTIONf_dihedral_angle_d23.2631634
X-RAY DIFFRACTIONf_chiral_restr0.123706
X-RAY DIFFRACTIONf_plane_restr0.007828
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.7964-2.92360.48771040.353720740.4877207473
2.9236-3.07770.39471200.318822490.3947224980
3.0777-3.27030.40121500.276123640.4012236484
3.2703-3.52260.37311320.278424030.3731240385
3.5226-3.87660.37421250.26223460.3742234682
3.8766-4.43640.27221430.1926140.2722261491
4.4364-5.58490.23441450.168527140.2344271494
5.5849-32.96080.28121390.232727990.2812279992
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.45970.3714-1.87251.1086-1.8241.3484-0.0253-0.0795-0.4326-0.99080.46620.08290.05570.7886-0.02870.8271-0.03850.22360.6863-0.08650.796422.4275-9.942634.9247
20.26990.6430.07581.0799-0.5671.7107-0.1974-0.05050.7826-1.00540.16911.1298-1.40590.60660.02520.37340.19070.0340.6785-0.11210.7569
30.73461.1379-0.65921.1081-0.91581.78620.00340.4437-0.18240.02760.32910.25840.5027-0.1252-0.10650.51630.0244-0.03030.3651-0.04170.3226
43.3263-0.5103-0.50670.92091.36181.4892-1.0637-0.4962-0.08280.23310.4405-0.0395-0.1399-0.16760.27280.445-0.06350.03370.35680.28120.2148
50.8995-0.7820.53421.146-0.23781.45130.4892-0.8101-0.0113-0.1243-0.00060.170.1158-0.1076-0.24330.5947-0.0373-0.10310.5270.0280.6465
61.341-0.3109-0.83841.41660.65081.94750.41070.0417-0.1397-0.14970.1559-0.3145-0.06840.1272-0.24050.35290.048-0.04850.4669-0.18570.5891
70.0173-0.0415-0.05461.7386-2.88533.605-0.0260.5061-0.18930.27090.37720.2523-0.966-0.0386-0.20850.7622-0.04280.29730.4161-0.05950.6463
80.6736-0.0164-0.45450.95720.78860.50870.04030.67981.7283-0.08761.7111-0.53680.4224-0.6551-0.19471.08620.113-0.07510.5022-0.05911.0201
9-0.0085-0.1052-0.35271.10430.12830.65990.2434-0.0260.33730.40090.0842-0.34360.10930.13740.06880.7490.09590.21710.47440.09110.7503
101.9293-0.77481.14681.02180.62080.75560.3477-0.4623-0.57190.08570.29640.01790.3913-0.0866-0.39660.67620.05650.01920.5930.2380.5703
111.05770.6682-0.41991.25-0.31430.67390.66-0.4245-0.0705-0.07-0.3550.3498-0.090.3103-0.21290.6955-0.09330.00750.57920.0780.6163
120.8899-1.8001-0.28711.3704-0.49513.80970.2013-0.12940.02530.17420.1694-0.12290.48820.678-0.22480.582-0.0828-0.12090.627-0.01320.6151
Refinement TLS groupSelection details: chain B and resid 205:281)

+
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