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- PDB-3d47: Crystal structure of L-rhamnonate dehydratase from Salmonella typ... -

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Basic information

Entry
Database: PDB / ID: 3d47
TitleCrystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg and D-malate
ComponentsPutative galactonate dehydratase
KeywordsLYASE / Structural Genomics / NYSGXRC / L-RHAMNONATE DEHYDRATASE / target 9265a / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


L-rhamnonate dehydratase / L-rhamnonate dehydratase activity / amino acid catabolic process / hydro-lyase activity / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
L-rhamnonate dehydratase / : / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like ...L-rhamnonate dehydratase / : / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
D-MALATE / L-rhamnonate dehydratase
Similarity search - Component
Biological speciesSalmonella typhimurium LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Sauder, J.M. / Burley, S.K. / Gerlt, J.A. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg and D-malate.
Authors: Fedorov, A.A. / Fedorov, E.V. / Sauder, J.M. / Burley, S.K. / Gerlt, J.A. / Almo, S.C.
History
DepositionMay 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 3, 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 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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 galactonate dehydratase
B: Putative galactonate dehydratase
C: Putative galactonate dehydratase
D: Putative galactonate dehydratase
E: Putative galactonate dehydratase
F: Putative galactonate dehydratase
G: Putative galactonate dehydratase
H: Putative galactonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)359,34824
Polymers358,0818
Non-polymers1,26716
Water30,9141716
1
A: Putative galactonate dehydratase
B: Putative galactonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8376
Polymers89,5202
Non-polymers3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-33.8 kcal/mol
Surface area26520 Å2
MethodPISA
2
C: Putative galactonate dehydratase
D: Putative galactonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8376
Polymers89,5202
Non-polymers3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-34.6 kcal/mol
Surface area26490 Å2
MethodPISA
3
E: Putative galactonate dehydratase
F: Putative galactonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8376
Polymers89,5202
Non-polymers3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-33.5 kcal/mol
Surface area26620 Å2
MethodPISA
4
G: Putative galactonate dehydratase
H: Putative galactonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8376
Polymers89,5202
Non-polymers3174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-33.5 kcal/mol
Surface area26420 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41240 Å2
ΔGint-211 kcal/mol
Surface area82950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.222, 122.003, 141.350
Angle α, β, γ (deg.)90.00, 108.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative galactonate dehydratase


Mass: 44760.066 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium LT2 (bacteria) / Strain: LT2 / SGSC1412 / Gene: yfaW, STM2291 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZNF9
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1716 / 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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEGi 3350, 0.15 M DL-Malic acid, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 29, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.8→24.88 Å / Num. all: 282894 / Num. obs: 282894 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.094

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BOX

3box


Resolution: 1.8→24.88 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1196758.18 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 14293 5.1 %RANDOM
Rwork0.202 ---
all0.205 282894 --
obs-282894 96.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.2199 Å2 / ksol: 0.363279 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.4 Å20 Å22.72 Å2
2---3.15 Å20 Å2
3----1.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25096 0 80 1716 26892
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.52
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.582.5
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.33 1162 5.2 %
Rwork0.286 21233 -
obs--76.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4MLT_xplor_par.txtMLT_xplor_top.txt
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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