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- PDB-1txl: Crystal structure of metal-binding protein yodA from E. coli, Pfa... -

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Basic information

Entry
Database: PDB / ID: 1txl
TitleCrystal structure of metal-binding protein yodA from E. coli, Pfam DUF149
ComponentsMetal-binding protein yodA
Keywordsstructural genomics / unknown function / yodA / E.coli / new fold / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


cellular response to zinc ion starvation / intracellular zinc ion homeostasis / cadmium ion binding / cellular response to cadmium ion / cellular response to hydrogen peroxide / outer membrane-bounded periplasmic space / zinc ion binding / metal ion binding / cytosol
Similarity search - Function
ZinT domain / ZinT (YodA) periplasmic lipocalin-like zinc-recruitment / Calycin beta-barrel core domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Metal-binding protein ZinT
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsEswaramoorthy, S. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical protein yodA
Authors: Eswaramoorthy, S. / Swaminathan, S.
History
DepositionJul 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal-binding protein yodA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7302
Polymers24,6651
Non-polymers651
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.240, 65.240, 41.340
Angle α, β, γ (deg.)90.00, 117.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Metal-binding protein yodA / Cadmium-induced protein yodA


Mass: 24664.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YODA, B1973 / Production host: Escherichia coli (E. coli) / References: UniProt: P76344
#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 / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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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: 1.9 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: PEG 1500, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12B10.979
SYNCHROTRONNSLS X12C21.2804, 1.2818, 1.2200
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJun 14, 2003
BRANDEIS - B42CCDJun 25, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2Si 111 CHANNELMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.28041
31.28181
41.221
ReflectionResolution: 1.69→50 Å / Num. all: 20672 / Num. obs: 20672 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 44.6
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.137 / Num. unique all: 1584 / % possible all: 73.9

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Processing

Software
NameVersionClassification
CBASSdata collection
SCALEPACKdata scaling
SOLVEphasing
SHARPphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 1.7→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: A Zn atom coordinating to HIS166, HIS175 and HIS177 has been located in the putative active-site cavity. Followed by Zn, continuous electron density has been observed. This density could ...Details: A Zn atom coordinating to HIS166, HIS175 and HIS177 has been located in the putative active-site cavity. Followed by Zn, continuous electron density has been observed. This density could accomodate a branched carbohydrate chain and a PO4 head group. A probable substrate suspected to be present in the structure has not been added to the model because it is not known for sure. Water molecules located around the Zn atom in the active site cavity have to be treated with care. Water molecule 218 may be replaced with a PO4.
RfactorNum. reflectionSelection details
Rfree0.2522 973 RANDOM
Rwork0.2282 --
obs0.2282 20185 -
all-20185 -
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1537 0 1 224 1762
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2451
X-RAY DIFFRACTIONc_bond_d0.0065

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