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- PDB-5w57: Structure of Holo AztC -

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Basic information

Entry
Database: PDB / ID: 5w57
TitleStructure of Holo AztC
ComponentsPeriplasmic solute binding protein
KeywordsMETAL BINDING PROTEIN / Solute binding protein / Zinc / ABC Transporter
Function / homology
Function and homology information


zinc ion transport / periplasmic space / cell adhesion / zinc ion binding
Similarity search - Function
: / Adhesin B / Adhesion lipoprotein / : / Periplasmic solute binding protein, ZnuA-like / Zinc-uptake complex component A periplasmic / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
High-affinity zinc uptake system protein AztC
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAvalos, D. / Yukl, E.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1SC2GM111170-01 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Mechanisms of zinc binding to the solute-binding protein AztC and transfer from the metallochaperone AztD.
Authors: Neupane, D.P. / Avalos, D. / Fullam, S. / Roychowdhury, H. / Yukl, E.T.
History
DepositionJun 14, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionSep 20, 2017ID: 4XRV
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic solute binding protein
B: Periplasmic solute binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8134
Polymers59,6832
Non-polymers1312
Water91951
1
A: Periplasmic solute binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9072
Polymers29,8411
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Periplasmic solute binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9072
Polymers29,8411
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-8 kcal/mol
Surface area23340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.840, 72.373, 105.613
Angle α, β, γ (deg.)90.00, 96.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Periplasmic solute binding protein


Mass: 29841.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (strain Pd 1222) (bacteria)
Strain: Pd 1222 / Gene: Pden_1597 / Cell line (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A1B2F3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.12 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7 / Details: Sodium Formate 4.0-4.5 M, Bis-tris propane 0.1 M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2017
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→48.92 Å / Num. obs: 34922 / % possible obs: 99.5 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.032 / Net I/σ(I): 12.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3427 / CC1/2: 0.903 / Rpim(I) all: 0.268 / % possible all: 90.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XRV

4xrv
PDB Unreleased entry


Resolution: 2.3→48.92 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.25
RfactorNum. reflection% reflection
Rfree0.2412 1743 5 %
Rwork0.2165 --
obs0.2178 34875 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4169 0 2 51 4222
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064276
X-RAY DIFFRACTIONf_angle_d0.8885841
X-RAY DIFFRACTIONf_dihedral_angle_d5.7812940
X-RAY DIFFRACTIONf_chiral_restr0.048664
X-RAY DIFFRACTIONf_plane_restr0.006789
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.36770.39361460.32662775X-RAY DIFFRACTION100
2.3677-2.44410.38991450.31552739X-RAY DIFFRACTION99
2.4441-2.53140.35491430.30712712X-RAY DIFFRACTION100
2.5314-2.63280.33931460.29772769X-RAY DIFFRACTION100
2.6328-2.75260.32221440.28542757X-RAY DIFFRACTION100
2.7526-2.89770.34031450.29582781X-RAY DIFFRACTION100
2.8977-3.07920.29841440.26362728X-RAY DIFFRACTION99
3.0792-3.31690.28671430.2572738X-RAY DIFFRACTION99
3.3169-3.65060.26911450.22412759X-RAY DIFFRACTION99
3.6506-4.17870.20261450.192748X-RAY DIFFRACTION99
4.1787-5.26370.19621470.16812789X-RAY DIFFRACTION99
5.2637-48.93430.17181500.17372837X-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)
12.3637-0.35530.60431.73710.35482.8427-0.01910.00390.19270.0807-0.28770.2465-0.1327-0.06040.27820.3042-0.0447-0.00380.5046-0.11570.40923.2667-0.27488.006
22.92571.7277-0.48693.0051.15712.8296-0.0515-0.32670.1889-0.3848-0.51420.7584-0.147-0.13190.55660.41940.1638-0.0370.5196-0.15090.52517.415310.602443.9866
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 25:308)
2X-RAY DIFFRACTION2(chain B and resseq 25:308)

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