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- PDB-2gp4: Structure of [FeS]cluster-free Apo Form of 6-Phosphogluconate Deh... -

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Basic information

Entry
Database: PDB / ID: 2gp4
TitleStructure of [FeS]cluster-free Apo Form of 6-Phosphogluconate Dehydratase from Shewanella oneidensis
Components6-phosphogluconate dehydratase
KeywordsLYASE / N-terminal domain largely alpha-helical / C-terminal domain mainly beta-sheet (trefoil-like) / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


phosphogluconate dehydratase / phosphogluconate dehydratase activity / Entner-Doudoroff pathway through 6-phosphogluconate / D-gluconate catabolic process / hydro-lyase activity / 4 iron, 4 sulfur cluster binding / metal ion binding / cytosol
Similarity search - Function
IlvD/EDD C-terminal domain-like / 6-phosphogluconate dehydratase / Dihydroxy-acid and 6-phosphogluconate dehydratases signature 2. / Dihydroxy-acid/6-phosphogluconate dehydratase, conserved site / Dihydroxy-acid and 6-phosphogluconate dehydratases signature 1. / Dihydroxy-acid/6-phosphogluconate dehydratase / IlvD/EDD, N-terminal domain / Dihydroxy-acid dehydratase, C-terminal / Dehydratase family / Glucose Oxidase; domain 1 ...IlvD/EDD C-terminal domain-like / 6-phosphogluconate dehydratase / Dihydroxy-acid and 6-phosphogluconate dehydratases signature 2. / Dihydroxy-acid/6-phosphogluconate dehydratase, conserved site / Dihydroxy-acid and 6-phosphogluconate dehydratases signature 1. / Dihydroxy-acid/6-phosphogluconate dehydratase / IlvD/EDD, N-terminal domain / Dihydroxy-acid dehydratase, C-terminal / Dehydratase family / Glucose Oxidase; domain 1 / 3-Layer(bba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Phosphogluconate dehydratase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.49 Å
AuthorsSchormann, N. / Symersky, J. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: Structure of [FeS]cluster-free Apo Form of 6-Phosphogluconate Dehydratase from Shewanella oneidensis
Authors: Schormann, N. / Symersky, J. / Karpova, E. / Zhang, Y. / Lu, S. / Qiu, S. / Bunzel, R. / Luan, C.-H. / Huang, W. / Luo, M. / Tsao, J. / Johnson, D. / Carson, M. / Zhou, Q. / Luo, D. / Gray, ...Authors: Schormann, N. / Symersky, J. / Karpova, E. / Zhang, Y. / Lu, S. / Qiu, S. / Bunzel, R. / Luan, C.-H. / Huang, W. / Luo, M. / Tsao, J. / Johnson, D. / Carson, M. / Zhou, Q. / Luo, D. / Gray, R. / Cao, Z. / An, J. / Arabshahi, A. / Li, S. / Stinnett, M. / McKinstry, A. / Lin, G. / Shang, Q. / Chen, Y. / DeLucas, L.
History
DepositionApr 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 6-phosphogluconate dehydratase
B: 6-phosphogluconate dehydratase


Theoretical massNumber of molelcules
Total (without water)135,3932
Polymers135,3932
Non-polymers00
Water9,962553
1
A: 6-phosphogluconate dehydratase


Theoretical massNumber of molelcules
Total (without water)67,6961
Polymers67,6961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 6-phosphogluconate dehydratase


Theoretical massNumber of molelcules
Total (without water)67,6961
Polymers67,6961
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: 6-phosphogluconate dehydratase

B: 6-phosphogluconate dehydratase


Theoretical massNumber of molelcules
Total (without water)135,3932
Polymers135,3932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
Buried area3870 Å2
ΔGint-37 kcal/mol
Surface area37670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.364, 118.649, 160.017
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: HIS / End label comp-ID: TYR / Refine code: 4 / Auth seq-ID: 0 - 608 / Label seq-ID: 20 - 628

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological assembly is likely a monomer. The asymmetric unit contains two monomers related by a non-crystallographic 2-fold.

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Components

#1: Protein 6-phosphogluconate dehydratase


Mass: 67696.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: edd / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: GenBank: 24348501, UniProt: Q8EEA0*PLUS, phosphogluconate dehydratase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 2.15 Å3/Da / Density % sol: 42.76 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 5% PEG400, 50mM cacodylate, 3mM DTT, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 8, 2004
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. all: 41534 / Num. obs: 41534 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.8 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 15.1
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.206 / Num. unique all: 4092 / Rsym value: 0.206 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.49→48.68 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.845 / SU B: 17.206 / SU ML: 0.214 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.629 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The N-terminal His-tag (-19 to -1) is not visible in the electron density except for His (0). The inactive apo protein (no substrate) is cluster-free. The N-terminal domain, which normally ...Details: The N-terminal His-tag (-19 to -1) is not visible in the electron density except for His (0). The inactive apo protein (no substrate) is cluster-free. The N-terminal domain, which normally contains the active site with a [4Fe-4S] cluster and a site for substrate-binding is largely disordered. Residues 34-89, 93-95, 106, 110-11, 181-199 and 226-230 are not visible in the electron density in chain a. in chain b residues 34-92, 106-107, 110-111, 155 and 181-230 are disordered and not visible in the electron density. In addition, side chains of residues 95, 97 and 98 in chain b are truncated because of missing electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.2908 2086 5 %RANDOM
Rwork0.2295 ---
all0.2325 39386 --
obs0.2325 39386 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.211 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2--0.45 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 2.49→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7563 0 0 553 8116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227670
X-RAY DIFFRACTIONr_angle_refined_deg1.11.98210391
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.86351005
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21824.43298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.609151300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4021547
X-RAY DIFFRACTIONr_chiral_restr0.0690.21237
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025666
X-RAY DIFFRACTIONr_nbd_refined0.1950.23902
X-RAY DIFFRACTIONr_nbtor_refined0.2950.25282
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2646
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.2134
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.216
X-RAY DIFFRACTIONr_mcbond_it0.5371.55185
X-RAY DIFFRACTIONr_mcangle_it0.80128021
X-RAY DIFFRACTIONr_scbond_it1.14632751
X-RAY DIFFRACTIONr_scangle_it1.6754.52370
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3642 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.30.5
medium thermal0.372
LS refinement shellResolution: 2.491→2.556 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 164 -
Rwork0.228 2734 -
obs-2898 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.4507-0.1977-0.08150.4102-0.01820.64-0.0554-0.02580.0017-0.00420.0508-0.0304-0.00220.00860.0045-0.0356-0.0093-0.0019-0.0138-0.0016-0.031823.086414.551623.5092
20.66670.3267-0.12930.50060.10370.7424-0.0146-0.0138-0.00740.0373-0.05410.00790.1028-0.03130.0687-0.0085-0.01390.0299-0.0508-0.0173-0.02198.5402-2.8088-16.6809
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 60820 - 628
2X-RAY DIFFRACTION2BB0 - 60820 - 628

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