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- PDB-4k2s: Crystal structure of the mutant P317A of d-mannonate dehydratase ... -

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Entry
Database: PDB / ID: 4k2s
TitleCrystal structure of the mutant P317A of d-mannonate dehydratase from chromohalobacter salexigens complexed with mg and d-gluconate
ComponentsD-mannonate dehydratase
KeywordsISOMERASE / Enolase fold / D-MANNONATE DEHYDRATASE / 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/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / 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/muconate lactonizing enzyme, conserved site / Mandelate racemase DgoD-like / 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-gluconic acid / D-galactonate dehydratase family member ManD
Similarity search - Component
Biological speciesChromohalobacter salexigens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of the mutant P317A of d-mannonate dehydratase from chromohalobacter salexigens complexed with mg and d-gluconate
Authors: Fedorov, A.A. / Fedorov, E.V. / Wichelecki, D. / Gerlt, J.A. / Almo, S.C.
History
DepositionApr 9, 2013Deposition site: RCSB / Processing site: RCSB
SupersessionApr 9, 2014ID: 3QKF
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_alt_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_auth_seq_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_alt_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.pdbx_ptnr2_label_alt_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-mannonate dehydratase
B: D-mannonate dehydratase
C: D-mannonate dehydratase
D: D-mannonate dehydratase
E: D-mannonate dehydratase
F: D-mannonate dehydratase
G: D-mannonate dehydratase
H: D-mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)365,72836
Polymers363,5388
Non-polymers2,19028
Water56,4413133
1
A: D-mannonate dehydratase
B: D-mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3858
Polymers90,8842
Non-polymers5016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-29 kcal/mol
Surface area26360 Å2
MethodPISA
2
C: D-mannonate dehydratase
E: D-mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,53711
Polymers90,8842
Non-polymers6539
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-40 kcal/mol
Surface area26470 Å2
MethodPISA
3
D: D-mannonate dehydratase
H: D-mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3858
Polymers90,8842
Non-polymers5016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-36 kcal/mol
Surface area26380 Å2
MethodPISA
4
F: D-mannonate dehydratase
G: D-mannonate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,4219
Polymers90,8842
Non-polymers5367
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-41 kcal/mol
Surface area26240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.334, 85.790, 195.638
Angle α, β, γ (deg.)90.00, 110.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-503-

MG

21C-503-

MG

31E-503-

MG

41G-503-

MG

51G-987-

HOH

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Components

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Protein / Sugars , 2 types, 16 molecules ABCDEFGH

#1: Protein
D-mannonate dehydratase


Mass: 45442.223 Da / Num. of mol.: 8 / Mutation: P317A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromohalobacter salexigens (bacteria) / Strain: DSM 3043 / ATCC BAA-138 / NCIMB 13768 / Gene: Csal_2974 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1QT89, mannonate dehydratase
#2: Sugar
ChemComp-GCO / D-gluconic acid / GLUCONIC ACID


Type: D-saccharide / Mass: 196.155 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O7

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Non-polymers , 4 types, 3153 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3133 / 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: 2.12 Å3/Da / Density % sol: 42.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% PEG 3350, 0.1M Succinic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.699→44.252 Å / Num. all: 332505 / Num. obs: 332505 / % possible obs: 99.35 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BSM

3bsm


Resolution: 1.699→44.252 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 20.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 16756 5.04 %RANDOM
Rwork0.1686 ---
all0.1703 332505 --
obs0.1703 332505 99.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.699→44.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24812 0 129 3133 28074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00725846
X-RAY DIFFRACTIONf_angle_d1.06735231
X-RAY DIFFRACTIONf_dihedral_angle_d13.0269244
X-RAY DIFFRACTIONf_chiral_restr0.0753826
X-RAY DIFFRACTIONf_plane_restr0.0054589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6986-1.71790.28734950.25139542X-RAY DIFFRACTION91
1.7179-1.73810.28555690.239510502X-RAY DIFFRACTION100
1.7381-1.75930.28545470.236910565X-RAY DIFFRACTION100
1.7593-1.78160.27596060.230610460X-RAY DIFFRACTION100
1.7816-1.8050.24875490.215910488X-RAY DIFFRACTION100
1.805-1.82970.2465530.20710569X-RAY DIFFRACTION100
1.8297-1.85590.24735510.206310525X-RAY DIFFRACTION100
1.8559-1.88360.25435730.209710562X-RAY DIFFRACTION100
1.8836-1.9130.40555690.380810318X-RAY DIFFRACTION98
1.913-1.94440.45925380.413910374X-RAY DIFFRACTION98
1.9444-1.97790.24425070.196110545X-RAY DIFFRACTION100
1.9779-2.01390.23565630.180810545X-RAY DIFFRACTION100
2.0139-2.05260.20925570.162310615X-RAY DIFFRACTION100
2.0526-2.09450.19895700.154810556X-RAY DIFFRACTION100
2.0945-2.140.1815820.145410533X-RAY DIFFRACTION100
2.14-2.18980.20375620.15510571X-RAY DIFFRACTION100
2.1898-2.24460.31765540.267510416X-RAY DIFFRACTION99
2.2446-2.30530.31395310.288610381X-RAY DIFFRACTION98
2.3053-2.37310.19415580.145510571X-RAY DIFFRACTION100
2.3731-2.44970.19095710.148210629X-RAY DIFFRACTION100
2.4497-2.53720.17855480.135410558X-RAY DIFFRACTION100
2.5372-2.63880.19175630.146110549X-RAY DIFFRACTION100
2.6388-2.75890.1835550.143810644X-RAY DIFFRACTION100
2.7589-2.90430.17155810.143510577X-RAY DIFFRACTION100
2.9043-3.08620.18655600.14510630X-RAY DIFFRACTION100
3.0862-3.32450.16515700.138610652X-RAY DIFFRACTION100
3.3245-3.65890.15145450.128810636X-RAY DIFFRACTION100
3.6589-4.1880.14575890.119210611X-RAY DIFFRACTION99
4.188-5.2750.12965610.107910732X-RAY DIFFRACTION100
5.275-44.26660.1465790.136610893X-RAY DIFFRACTION100
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)
10.51150.13280.00070.25440.03660.3424-0.00270.02890.0716-0.01840.00260.1013-0.0758-0.09060.00120.07180.0351-0.01290.1110.00890.13414.527-5.112-102.058
20.26-0.07350.05840.3473-0.16680.56460.00590.0445-0.0467-0.09160.00810.06650.0858-0.0816-0.01190.0809-0.0109-0.02430.0992-0.01370.106816.486-32.308-117.614
30.2866-0.1231-0.04510.2176-0.00020.53690.01590.03740.0461-0.0895-0.0083-0.0784-0.21050.1384-0.0070.2437-0.06830.02730.140.00470.111622.396-41.49-22.266
40.40750.11170.10580.23550.05170.4097-0.01280.06190.0563-0.0710.01210.0546-0.1749-0.0651-0.0030.22760.0325-0.02240.120.01250.096-22.108-41.558-22.396
50.55010.2110.03720.46970.02920.45490.00380.0349-0.0741-0.03320.0116-0.10750.01170.1236-0.01730.10660.00650.00870.1187-0.00980.103931.122-68.8-4.564
60.4562-0.1695-0.04770.34380.08970.32580.0008-0.0592-0.08280.07080.00160.11070.0357-0.0742-0.00080.073-0.01550.02070.1080.01620.12428.194-32.349-73.964
70.26730.05860.02590.3476-0.19110.5543-0.0085-0.06150.05350.11320.00450.0431-0.1213-0.06570.00310.1120.02060.01650.0976-0.02160.094823.713-4.859-62.042
80.249-0.015-0.03870.3506-0.15280.6335-0.01170.079-0.0495-0.1450.00990.01560.0544-0.02870.00030.1901-0.0112-0.01270.1101-0.02620.0896-4.705-68.841-31.199
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 405
2X-RAY DIFFRACTION2B3 - 405
3X-RAY DIFFRACTION3C2 - 405
4X-RAY DIFFRACTION4D3 - 405
5X-RAY DIFFRACTION5E2 - 405
6X-RAY DIFFRACTION6F3 - 405
7X-RAY DIFFRACTION7G3 - 405
8X-RAY DIFFRACTION8H2 - 405

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