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- PDB-3tio: Crystal structures of yrdA from Escherichia coli, a homologous pr... -

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Basic information

Entry
Database: PDB / ID: 3tio
TitleCrystal structures of yrdA from Escherichia coli, a homologous protein of gamma-class carbonic anhydrase, show possible allosteric conformations
ComponentsProtein YrdA
KeywordsTRANSFERASE / Carbonic anhydrase (CA) catalyzes / zinc ion binding
Function / homology
Function and homology information


protein-containing complex / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
: / : / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Protein YrdA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsPark, H.M. / Choi, J.W. / Lee, J.E. / Jung, C.H. / Kim, B.Y. / Kim, J.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structures of the gamma-class carbonic anhydrase homologue YrdA suggest a possible allosteric switch
Authors: Park, H.M. / Park, J.H. / Choi, J.W. / Lee, J.E. / Kim, B.Y. / Jung, C.H. / Kim, J.S.
History
DepositionAug 21, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2012Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Protein YrdA
B: Protein YrdA
C: Protein YrdA
D: Protein YrdA
E: Protein YrdA
F: Protein YrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,47316
Polymers120,7016
Non-polymers77210
Water21,9061216
1
A: Protein YrdA
B: Protein YrdA
C: Protein YrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7368
Polymers60,3503
Non-polymers3865
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-170 kcal/mol
Surface area19650 Å2
MethodPISA
2
D: Protein YrdA
E: Protein YrdA
F: Protein YrdA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7368
Polymers60,3503
Non-polymers3865
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-169 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.976, 84.384, 97.758
Angle α, β, γ (deg.)90.00, 93.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein YrdA


Mass: 20116.754 Da / Num. of mol.: 6 / Mutation: R6H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yrdA, b3279, JW5710 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9W9
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1216 / 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: 1.91 Å3/Da / Density % sol: 35.6 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 4.6
Details: 20 % (w/v) polyethyleneglycol Monomethyl Ether 2000, 0.15M (NH4)2SO4, 0.1M Sodium Acetate, pH 4.6, EVAPORATION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.41→50 Å / Num. obs: 173327 / % possible obs: 99.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.41→1.43 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V3W

1v3w


Resolution: 1.41→50 Å / σ(F): -3
RfactorNum. reflectionSelection details
Rfree0.2098 12497 RNADOM
Rwork0.1927 --
obs0.1927 171646 -
Refinement stepCycle: LAST / Resolution: 1.41→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8111 0 26 1216 9353
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004184
X-RAY DIFFRACTIONc_angle_d1.35635

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