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- PDB-3ij6: CRYSTAL STRUCTURE OF AN UNCHARACTERIZED METAL-DEPENDENT HYDROLASE... -

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Basic information

Entry
Database: PDB / ID: 3ij6
TitleCRYSTAL STRUCTURE OF AN UNCHARACTERIZED METAL-DEPENDENT HYDROLASE FROM Lactobacillus acidophilus
ComponentsUNCHARACTERIZED METAL-DEPENDENT HYDROLASE
KeywordsHYDROLASE / STRUCTURAL GENOMICS / AMIDOHYDROLASE / PSI-2 / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC
Function / homology
Function and homology information


carboxy-lyase activity / hydrolase activity / metal ion binding
Similarity search - Function
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase / Amidohydrolase / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Putative 4-oxalomesaconate hydratase
Similarity search - Component
Biological speciesLactobacillus acidophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsPatskovsky, Y. / Toro, R. / Dickey, M. / Chang, S. / Sauder, J.M. / Raushel, F.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF AN UNCHARACTERIZED METAL-DEPENDENT HYDROLASE FROM Lactobacillus acidopphilus
Authors: Patskovsky, Y. / Toro, R. / Dickey, M. / Chang, S. / Sauder, J.M. / Raushel, F.M. / Burley, S.K. / Almo, S.C.
History
DepositionAug 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UNCHARACTERIZED METAL-DEPENDENT HYDROLASE
B: UNCHARACTERIZED METAL-DEPENDENT HYDROLASE
C: UNCHARACTERIZED METAL-DEPENDENT HYDROLASE
D: UNCHARACTERIZED METAL-DEPENDENT HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,80712
Polymers141,4534
Non-polymers3548
Water6,918384
1
A: UNCHARACTERIZED METAL-DEPENDENT HYDROLASE
B: UNCHARACTERIZED METAL-DEPENDENT HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9036
Polymers70,7272
Non-polymers1774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-125 kcal/mol
Surface area22570 Å2
MethodPISA
2
C: UNCHARACTERIZED METAL-DEPENDENT HYDROLASE
D: UNCHARACTERIZED METAL-DEPENDENT HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9036
Polymers70,7272
Non-polymers1774
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-125 kcal/mol
Surface area22450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.717, 96.433, 96.033
Angle α, β, γ (deg.)90.00, 90.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-388-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

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Components

#1: Protein
UNCHARACTERIZED METAL-DEPENDENT HYDROLASE / Putative 4-oxalomesaconate hydratase


Mass: 35363.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus acidophilus (bacteria) / Gene: LBA1049 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5FK79
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growpH: 4.5
Details: 0.1M SODIUM ACETATE, PH 4.5, 25% PEG3350, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.994→50 Å / Num. obs: 106038 / % possible obs: 99.1 % / Observed criterion σ(I): -5 / Redundancy: 2.1 % / Biso Wilson estimate: 30.79 Å2 / Rsym value: 0.097 / Net I/σ(I): 5.5
Reflection shellResolution: 1.99→2.07 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 0.7 / % possible all: 93.1

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Processing

Software
NameVersionClassification
SHELXmodel building
RESOLVEmodel building
REFMAC5.3.0034refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.966 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26812 3132 3 %RANDOM
Rwork0.22062 ---
obs0.22205 101373 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.667 Å2
Baniso -1Baniso -2Baniso -3
1-2.27 Å20 Å20.16 Å2
2---2.19 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9741 0 8 384 10133
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0229997
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.95713603
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88951244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.47125.726468
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.434151753
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0141520
X-RAY DIFFRACTIONr_chiral_restr0.0860.21524
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027580
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1450.34948
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.56811
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.5932
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0340.52
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1020.351
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.45426134
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.02739978
X-RAY DIFFRACTIONr_scbond_it7.37933963
X-RAY DIFFRACTIONr_scangle_it9.47553605
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2309 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.350.2
tight positional0.270
tight positional0.290
tight positional0.290
tight thermal7.652.5
tight thermal9.030
tight thermal7.830
tight thermal8.960
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 220 -
Rwork0.314 7196 -
obs--97.03 %

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