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- PDB-3laz: The crystal structure of the N-terminal domain of D-galactarate d... -

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Basic information

Entry
Database: PDB / ID: 3laz
TitleThe crystal structure of the N-terminal domain of D-galactarate dehydratase from Escherichia coli CFT073
ComponentsD-galactarate dehydratase
KeywordsLYASE / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


galactarate dehydratase / D-galacturonate catabolic process / galactarate catabolic process / galactarate dehydratase activity / ferrous iron binding / protein homodimerization activity
Similarity search - Function
Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #110 / Galactarate dehydratase GarD-like / Galactarate dehydratase (L-threo-forming) GarD, Enterobacteriaceae / UxaA/GarD, SAF domain / : / D-galactarate/Altronate dehydratase, C-terminal / D-galactarate/Altronate dehydratase, C-terminal / D-galactarate dehydratase/Altronate hydrolase, second domain / SAF domain / SAF domain ...Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 - #110 / Galactarate dehydratase GarD-like / Galactarate dehydratase (L-threo-forming) GarD, Enterobacteriaceae / UxaA/GarD, SAF domain / : / D-galactarate/Altronate dehydratase, C-terminal / D-galactarate/Altronate dehydratase, C-terminal / D-galactarate dehydratase/Altronate hydrolase, second domain / SAF domain / SAF domain / SAF / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Roll / Mainly Beta
Similarity search - Domain/homology
Galactarate dehydratase (L-threo-forming) / Galactarate dehydratase (L-threo-forming)
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.921 Å
AuthorsTan, K. / Li, H. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the N-terminal domain of D-galactarate dehydratase from Escherichia coli CFT073
Authors: Tan, K. / Li, H. / Bearden, J. / Joachimiak, A.
History
DepositionJan 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-galactarate dehydratase
B: D-galactarate dehydratase


Theoretical massNumber of molelcules
Total (without water)21,9102
Polymers21,9102
Non-polymers00
Water1,45981
1
A: D-galactarate dehydratase

A: D-galactarate dehydratase


Theoretical massNumber of molelcules
Total (without water)21,9102
Polymers21,9102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/41
Buried area2350 Å2
ΔGint-11 kcal/mol
Surface area10760 Å2
MethodPISA
2
B: D-galactarate dehydratase

B: D-galactarate dehydratase


Theoretical massNumber of molelcules
Total (without water)21,9102
Polymers21,9102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554x,-y,-z-1/21
Buried area2340 Å2
ΔGint-6 kcal/mol
Surface area10680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.279, 106.279, 51.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
DetailsExperimentally unknown. likely to form a dimer.

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Components

#1: Protein D-galactarate dehydratase


Mass: 10955.176 Da / Num. of mol.: 2 / Fragment: N-terminal domain, residues 1-96
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFT073 / Gene: c3883, yhaG / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037
References: UniProt: Q8FDB6, UniProt: P39829*PLUS, galactarate dehydratase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris pH 3.0M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2009 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.92→48 Å / Num. all: 22935 / Num. obs: 22935 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 52.5
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.743 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1066 / % possible all: 94.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.921→47.529 Å / SU ML: 0.22 / σ(F): 0.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2451 1080 5.12 %random
Rwork0.2033 ---
all0.2053 21079 --
obs0.2053 21079 91.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.076 Å2 / ksol: 0.368 e/Å3
Refinement stepCycle: LAST / Resolution: 1.921→47.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1488 0 0 81 1569
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061517
X-RAY DIFFRACTIONf_angle_d1.0882063
X-RAY DIFFRACTIONf_dihedral_angle_d17.609555
X-RAY DIFFRACTIONf_chiral_restr0.072238
X-RAY DIFFRACTIONf_plane_restr0.004269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9208-2.00820.36381190.32791973X-RAY DIFFRACTION74
2.0082-2.11410.31021240.24882284X-RAY DIFFRACTION85
2.1141-2.24660.25751080.21292421X-RAY DIFFRACTION89
2.2466-2.420.24711600.22422444X-RAY DIFFRACTION92
2.42-2.66350.28161440.22452557X-RAY DIFFRACTION95
2.6635-3.04890.28061480.24012647X-RAY DIFFRACTION97
3.0489-3.8410.24961320.19442740X-RAY DIFFRACTION99
3.841-47.54390.19771450.17292933X-RAY DIFFRACTION100
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1refined4.05660.2396-1.2210.0191-0.23114.06490.10270.2667-0.3082-0.1123-0.0252-0.02131.4981-0.00510.05340.5092-0.0149-0.00450.2780.03180.350341.127717.6931-19.5843
22.6598-0.72841.69582.0814-0.47084.92270.0613-0.2482-0.0194-0.2872-0.0178-0.1020.3017-0.0224-0.02470.38070.02320.03970.32270.00820.303
35.79940.15941.18226.97161.27067.6860.3316-0.5724-0.36920.3342-0.3255-0.0201-0.7164-0.8251-0.24460.41310.00040.06810.4069-0.02760.3732
40.55950.4568-0.77390.3763-0.97637.09760.23290.14160.08410.0057-0.0770.0841-0.12530.0614-0.13890.58670.1852-0.01070.3523-0.01840.3098
Refinement TLS groupSelection details: chain B resid 12:93

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