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- PDB-6n01: Structure of apo AztD from Citrobacter koseri -

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Basic information

Entry
Database: PDB / ID: 6n01
TitleStructure of apo AztD from Citrobacter koseri
ComponentsAztD Protein
KeywordsCHAPERONE / periplasm / beta propeller / zinc / metallochaperone
Function / homology: / Nitrous oxide reductase, N-terminal / periplasmic space / WD40/YVTN repeat-like-containing domain superfamily / metal ion binding / TRIETHYLENE GLYCOL / Zinc chaperone AztD
Function and homology information
Biological speciesCitrobacter koseri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsYukl, E.T. / Neupane, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM122819 United States
CitationJournal: Commun Biol / Year: 2019
Title: Crystal structures of AztD provide mechanistic insights into direct zinc transfer between proteins.
Authors: Neupane, D.P. / Fullam, S.H. / Chacon, K.N. / Yukl, E.T.
History
DepositionNov 6, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: AztD Protein
A: AztD Protein
C: AztD Protein
D: AztD Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,4899
Polymers181,8694
Non-polymers6205
Water9,026501
1
B: AztD Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6182
Polymers45,4671
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: AztD Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6182
Polymers45,4671
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: AztD Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5292
Polymers45,4671
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: AztD Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,7253
Polymers45,4671
Non-polymers2572
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.866, 127.854, 113.155
Angle α, β, γ (deg.)90.00, 94.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
AztD Protein


Mass: 45467.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter koseri (strain ATCC BAA-895 / CDC 4225-83 / SGSC4696) (bacteria)
Strain: ATCC BAA-895 / CDC 4225-83 / SGSC4696 / Gene: CKO_00948 / Production host: Escherichia coli (E. coli) / References: UniProt: A8AF35
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 292 K / Method: batch mode / pH: 6
Details: 10 mg/mL protein was combined in a 1:1 ratio with 24% PEG 4000, 0.1 M sodium nitrate, 0.1 M MES pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2018
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: 1.98→48.43 Å / Num. obs: 110365 / % possible obs: 98.6 % / Redundancy: 3.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.044 / Rrim(I) all: 0.085 / Χ2: 0.9 / Net I/σ(I): 9.7
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 16782 / CC1/2: 0.758 / Rpim(I) all: 0.326 / Rrim(I) all: 0.621 / Χ2: 0.69 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6cmk

6cmk


Resolution: 1.98→48.431 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2379 2003 1.82 %
Rwork0.1945 --
obs0.1954 110300 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→48.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11040 0 40 501 11581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01311340
X-RAY DIFFRACTIONf_angle_d1.25915407
X-RAY DIFFRACTIONf_dihedral_angle_d12.1496830
X-RAY DIFFRACTIONf_chiral_restr0.0721774
X-RAY DIFFRACTIONf_plane_restr0.0092007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.02950.33051420.27587590X-RAY DIFFRACTION96
2.0295-2.08440.35391330.26747522X-RAY DIFFRACTION96
2.0844-2.14570.26971340.24827536X-RAY DIFFRACTION97
2.1457-2.2150.29511490.22947697X-RAY DIFFRACTION98
2.215-2.29420.25641420.2227710X-RAY DIFFRACTION98
2.2942-2.3860.25351430.21537724X-RAY DIFFRACTION99
2.386-2.49460.26231510.21647794X-RAY DIFFRACTION99
2.4946-2.62610.25841410.21637779X-RAY DIFFRACTION99
2.6261-2.79060.27571440.22017823X-RAY DIFFRACTION100
2.7906-3.00610.26881450.21927843X-RAY DIFFRACTION100
3.0061-3.30850.26091410.20087792X-RAY DIFFRACTION100
3.3085-3.78710.2151410.17797833X-RAY DIFFRACTION99
3.7871-4.77070.18911470.14737780X-RAY DIFFRACTION99
4.7707-48.44580.1981500.17027874X-RAY DIFFRACTION99

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