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- PDB-3og9: Structure of YahD with Malic acid -

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Basic information

Entry
Database: PDB / ID: 3og9
TitleStructure of YahD with Malic acid
Componentsprotein yahD a copper inducible hydrolase
KeywordsHYDROLASE / alpha/beta hydrolase / copper homeostasis / malic acid
Function / homology
Function and homology information


Dienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-MALATE / Dienelactone hydrolase domain-containing protein
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMartinez Font, J. / Mancini, S. / Tauberger, E. / Moniot, S.
CitationJournal: Fems Microbiol.Lett. / Year: 2011
Title: Regulation and structure of YahD, a copper inducible alpha/beta hydrolase of Lactococcus lactis IL1403
Authors: Martinez, J. / Mancini, S. / Tauberger, E. / Weise, C. / Saenger, W. / Solioz, M.
History
DepositionAug 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Sep 6, 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 / 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 / _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

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Assembly

Deposited unit
A: protein yahD a copper inducible hydrolase
B: protein yahD a copper inducible hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4454
Polymers47,1772
Non-polymers2682
Water8,773487
1
A: protein yahD a copper inducible hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7232
Polymers23,5891
Non-polymers1341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: protein yahD a copper inducible hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7232
Polymers23,5891
Non-polymers1341
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.640, 79.070, 130.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein protein yahD a copper inducible hydrolase


Mass: 23588.654 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Strain: IL1403 / Gene: yahD, LL0076, L795, L79507 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9CJC1
#2: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT THE UNP ENTRY Q9CJC1 SHOULD HAVE RESIDUES 191T AND 199K

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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: 2.21 Å3/Da / Density % sol: 44.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 37.5% PEG 3350, 150mM DL-Malic acid pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 9, 2009
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.88→40 Å / Num. obs: 34965 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.139 / Net I/σ(I): 0.159
Reflection shellResolution: 1.88→1.93 Å / Rmerge(I) obs: 0.691 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.3.0040refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 2hli

2hli


Resolution: 1.88→39.53 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.158 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22422 1749 5 %RANDOM
Rwork0.16944 ---
obs0.17216 33213 100 %-
all-34965 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.441 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.88→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3275 0 18 487 3780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223480
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9654721
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3215441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.73325.647170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36215625
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.941512
X-RAY DIFFRACTIONr_chiral_restr0.1070.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022672
X-RAY DIFFRACTIONr_nbd_refined0.2060.21628
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22400
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2441
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.262
X-RAY DIFFRACTIONr_mcbond_it1.0431.52208
X-RAY DIFFRACTIONr_mcangle_it1.53823440
X-RAY DIFFRACTIONr_scbond_it2.51331436
X-RAY DIFFRACTIONr_scangle_it3.8414.51281
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 127 -
Rwork0.203 2410 -
obs--100 %

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