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- PDB-3dxi: Crystal structure of the N-terminal domain of a putative aldolase... -

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Basic information

Entry
Database: PDB / ID: 3dxi
TitleCrystal structure of the N-terminal domain of a putative aldolase (BVU_2661) from Bacteroides vulgatus
ComponentsPutative aldolase
Keywordsstructural genomics / unknown function / TIM barrel / 11107n / PSI2 / NYSGXRC / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


2-isopropylmalate synthase activity / L-leucine biosynthetic process
Similarity search - Function
: / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacteroides vulgatus ATCC 8482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsEswaramoorthy, S. / Pabalan, A.A. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of the N-terminal domain of a putative aldolase (BVU_2661) from Bacteroides vulgatus
Authors: Eswaramoorthy, S. / Pabalan, A.A. / Burley, S.K. / Swaminathan, S.
History
DepositionJul 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative aldolase
B: Putative aldolase


Theoretical massNumber of molelcules
Total (without water)74,2172
Polymers74,2172
Non-polymers00
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-20 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.258, 65.639, 177.835
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 Putative aldolase


Mass: 37108.629 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Details: BC - pSGX3 (BC)
Source: (gene. exp.) Bacteroides vulgatus ATCC 8482 (bacteria)
Gene: BVU_2661 / Plasmid: pSGX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL-Stratagene / References: UniProt: A6L3P9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG3350, Ammonium Acetate, Sodium Citrate, Ethyl acetate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 18, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.04→50 Å / Num. all: 42720 / Num. obs: 42720 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.1 % / Biso Wilson estimate: 7.5 Å2 / Rmerge(I) obs: 0.136
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.539 / Num. unique all: 4090 / % possible all: 95.8

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELX& SHARPmodel building
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
SHELX& SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.04→36.81 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2316 1641 -RANDOM
Rwork0.1965 ---
all0.223 40397 --
obs0.223 40397 92.7 %-
Displacement parametersBiso mean: 16.1 Å2
Baniso -1Baniso -2Baniso -3
1--4.18 Å20 Å20 Å2
2--9.04 Å20 Å2
3----4.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.04→36.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4744 0 0 457 5201
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_deg0.82
LS refinement shellResolution: 2.04→2.17 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.281 247 -
Rwork0.229 --
obs-6002 84.2 %

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