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- PDB-1oej: YodA from Escherichia coli crystallised with no added ions -

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Basic information

Entry
Database: PDB / ID: 1oej
TitleYodA from Escherichia coli crystallised with no added ions
ComponentsHYPOTHETICAL PROTEIN YODA
KeywordsSTRESS PROTEIN/LIPOCALIN / STRESS PROTEIN / LIPOCALIN / YODA / STRESS PROTEIN-LIPOCALIN complex
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
NICKEL (II) ION / Metal-binding protein ZinT
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsDavid, G. / Blondeau, K. / Renouard, M. / Penel, S. / Lewit-Bentley, A.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Yoda from Escherichia Coli is a Metal-Binding, Lipocalin-Like Protein
Authors: David, G. / Blondeau, K. / Schiltz, M. / Penel, S. / Lewit-Bentley, A.
History
DepositionMar 27, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN YODA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4332
Polymers22,3741
Non-polymers591
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)40.348, 64.558, 41.499
Angle α, β, γ (deg.)90.00, 117.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HYPOTHETICAL PROTEIN YODA


Mass: 22373.879 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ESCHERICHIA COLI (E. coli) / References: UniProt: P76344
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE: MAIRLYKLAVALGVFIVSAPAFS THAT IS INCLUDED THE SWISPROT RECORD UPSTREAM OF THE SEQUENCE ...THE SEQUENCE: MAIRLYKLAVALGVFIVSAPAFS THAT IS INCLUDED THE SWISPROT RECORD UPSTREAM OF THE SEQUENCE CRYSTALLISED, CORRESPONDS TO A SIGNAL SEQUENCE THAT IS CLEAVED IN THE MATURE PROTEIN.

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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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growpH: 6.5
Details: 10 MG/ML PROTEIN, 30% PEG 10000, 100 MM SODIUM CACODYLATE, PH = 6.5 200 MM SODIUM ACETATE
Crystal grow
*PLUS
Method: other / Details: David, G., (2002) Acta Cryst., D58, 1243.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1.3
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 2001 / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.81→14.92 Å / Num. obs: 6027 / % possible obs: 74.5 % / Redundancy: 1.6 % / Biso Wilson estimate: 20.107 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.5
Reflection shellResolution: 1.81→1.91 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 1.6 / % possible all: 69.7
Reflection
*PLUS
Highest resolution: 1.81 Å

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CCP4phasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OEE

1oee


Resolution: 1.81→36.76 Å / SU B: 4.702 / SU ML: 0.138 / Cross valid method: THROUGHOUT / ESU R: 0.199 / ESU R Free: 0.189
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FIRST 6 RESIDUES AT THE N-TERMINUS ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.25226 653 5.1 %RANDOM
Rwork0.18 ---
obs0.18371 12128 74.27 %-
Displacement parametersBiso mean: 27.508 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å2-0.52 Å2
2--0.83 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.81→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 1 101 1628
Refinement
*PLUS
Highest resolution: 1.8 Å / Rfactor Rfree: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.018
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg1.467
X-RAY DIFFRACTIONplane_restr0.006

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