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- PDB-3p93: Crystal structure of D-mannonate dehydratase from Chromohalobacte... -

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Basic information

Entry
Database: PDB / ID: 3p93
TitleCrystal structure of D-mannonate dehydratase from Chromohalobacter Salexigens complexed with MG,D-Mannonate and 2-keto-3-deoxy-D-Gluconate
ComponentsMandelate racemase/muconate lactonizing enzyme
KeywordsISOMERASE / Enolase fold / multifunctional enzyme / Enolase superfamily / D-Mannonate / D-Gluconate
Function / homology
Function and homology information


gluconate dehydratase / gluconate dehydratase activity / mannonate dehydratase / mannonate dehydratase activity / Lyases; Carbon-oxygen lyases; Hydro-lyases / amino acid catabolic process / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
: / D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase DgoD-like / 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 ...: / D-mannonate dehydratase-like / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase DgoD-like / 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-MANNONIC ACID / 2-KETO-3-DEOXYGLUCONATE / D-galactonate dehydratase family member ManD
Similarity search - Component
Biological speciesChromohalobacter salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C.
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF D-MANNONATE DEHYDRATASE FROM CHROMOHALOBACTER SALEXIGENS complexed with MG,D-Mannonate and 2-keto-3-deoxy-D-Gluconate
Authors: Fedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C.
History
DepositionOct 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
C: Mandelate racemase/muconate lactonizing enzyme
D: Mandelate racemase/muconate lactonizing enzyme
E: Mandelate racemase/muconate lactonizing enzyme
F: Mandelate racemase/muconate lactonizing enzyme
G: Mandelate racemase/muconate lactonizing enzyme
H: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)365,43824
Polymers363,7468
Non-polymers1,69216
Water33,7061871
1
A: Mandelate racemase/muconate lactonizing enzyme
H: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3596
Polymers90,9372
Non-polymers4234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-37 kcal/mol
Surface area26420 Å2
MethodPISA
2
B: Mandelate racemase/muconate lactonizing enzyme
D: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3596
Polymers90,9372
Non-polymers4234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-37 kcal/mol
Surface area26420 Å2
MethodPISA
3
C: Mandelate racemase/muconate lactonizing enzyme
G: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3416
Polymers90,9372
Non-polymers4054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-36 kcal/mol
Surface area26360 Å2
MethodPISA
4
E: Mandelate racemase/muconate lactonizing enzyme
F: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3776
Polymers90,9372
Non-polymers4414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-37 kcal/mol
Surface area26260 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51180 Å2
ΔGint-183 kcal/mol
Surface area79770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.242, 167.263, 168.863
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer

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Components

#1: Protein
Mandelate racemase/muconate lactonizing enzyme


Mass: 45468.258 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromohalobacter salexigens (bacteria) / Gene: Csal_2974 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1QT89
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CS2 / D-MANNONIC ACID / D-MANNONATE


Mass: 196.155 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O7
#4: Chemical
ChemComp-KDG / 2-KETO-3-DEOXYGLUCONATE


Mass: 178.140 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H10O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1871 / 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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.3 M magnesium formate, 0.1M bis-tris, pH 5.5, 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: Oct 7, 2010
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→41.816 Å / Num. all: 286929 / Num. obs: 286929 / % possible obs: 99.84 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OW1

3ow1


Resolution: 1.8→41.816 Å / SU ML: 0.25 / σ(F): 0 / Phase error: 23.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 14508 5.06 %RANDOM
Rwork0.1988 ---
all0.2009 286929 --
obs0.2009 286929 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.981 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.4993 Å20 Å20 Å2
2---0.2746 Å20 Å2
3---4.7739 Å2
Refinement stepCycle: LAST / Resolution: 1.8→41.816 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24384 0 108 1871 26363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00725158
X-RAY DIFFRACTIONf_angle_d1.10634268
X-RAY DIFFRACTIONf_dihedral_angle_d16.2118978
X-RAY DIFFRACTIONf_chiral_restr0.0823709
X-RAY DIFFRACTIONf_plane_restr0.0054463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82050.37094770.32938791X-RAY DIFFRACTION97
1.8205-1.84190.34044600.30548946X-RAY DIFFRACTION99
1.8419-1.86430.33994690.29058990X-RAY DIFFRACTION100
1.8643-1.88790.32525290.2888912X-RAY DIFFRACTION100
1.8879-1.91280.34174980.27819033X-RAY DIFFRACTION100
1.9128-1.9390.31594900.26419042X-RAY DIFFRACTION100
1.939-1.96670.29874920.25069007X-RAY DIFFRACTION100
1.9667-1.9960.30254840.24159025X-RAY DIFFRACTION100
1.996-2.02720.30664590.23179013X-RAY DIFFRACTION100
2.0272-2.06050.26624640.21689070X-RAY DIFFRACTION100
2.0605-2.0960.27185080.21499001X-RAY DIFFRACTION100
2.096-2.13410.25745120.1969028X-RAY DIFFRACTION100
2.1341-2.17510.26614950.19649020X-RAY DIFFRACTION100
2.1751-2.21950.25255140.19529053X-RAY DIFFRACTION100
2.2195-2.26780.24464670.18669021X-RAY DIFFRACTION100
2.2678-2.32050.23324810.1839059X-RAY DIFFRACTION100
2.3205-2.37860.24474600.18679090X-RAY DIFFRACTION100
2.3786-2.44290.24424530.19029114X-RAY DIFFRACTION100
2.4429-2.51480.23724730.18189099X-RAY DIFFRACTION100
2.5148-2.59590.23754680.18399089X-RAY DIFFRACTION100
2.5959-2.68870.24734970.18139066X-RAY DIFFRACTION100
2.6887-2.79630.22634670.17719124X-RAY DIFFRACTION100
2.7963-2.92350.23344990.17959082X-RAY DIFFRACTION100
2.9235-3.07760.22284780.17869134X-RAY DIFFRACTION100
3.0776-3.27040.22024910.1789121X-RAY DIFFRACTION100
3.2704-3.52280.21164990.17059151X-RAY DIFFRACTION100
3.5228-3.87710.18184700.16059191X-RAY DIFFRACTION100
3.8771-4.43750.18394900.16059250X-RAY DIFFRACTION100
4.4375-5.58870.21664830.18029310X-RAY DIFFRACTION100
5.5887-41.8270.2244810.2379589X-RAY DIFFRACTION100

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