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- PDB-5mvi: Crystal structure of 2-methylcitrate dehydratase (PrpD) from Salm... -

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Basic information

Entry
Database: PDB / ID: 5mvi
TitleCrystal structure of 2-methylcitrate dehydratase (PrpD) from Salmonella enterica
Components2-methylcitrate dehydratase
KeywordsLYASE / DEHYDRATASE
Function / homology
Function and homology information


2-methylcitrate dehydratase / 2-methylcitrate dehydratase activity / propionate metabolic process, methylcitrate cycle / aconitate hydratase / aconitate hydratase activity / propionate catabolic process, 2-methylcitrate cycle / tricarboxylic acid cycle / 2 iron, 2 sulfur cluster binding
Similarity search - Function
2-methylcitrate dehydratase PrpD / 2-methylcitrate dehydratase PrpD / 2-methylcitrate dehydratase PrpD / 2-methylcitrate dehydratase PrpD / MmgE/PrpD / MmgE/PrpD superfamily / MmgE/PrpD superfamily, domain 1 / MmgE/PrpD superfamily, domain 2 / MmgE/PrpD, N-terminal / MmgE/PrpD, C-terminal ...2-methylcitrate dehydratase PrpD / 2-methylcitrate dehydratase PrpD / 2-methylcitrate dehydratase PrpD / 2-methylcitrate dehydratase PrpD / MmgE/PrpD / MmgE/PrpD superfamily / MmgE/PrpD superfamily, domain 1 / MmgE/PrpD superfamily, domain 2 / MmgE/PrpD, N-terminal / MmgE/PrpD, C-terminal / MmgE/PrpD N-terminal domain / MmgE/PrpD C-terminal domain / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / 2-methylcitrate dehydratase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.05 Å
AuthorsRace, P.R. / Baker, G.E.
CitationJournal: To Be Published
Title: Crystal structure of 2-methylcitrate dehydratase (PrpD) from Salmonella enterica
Authors: Race, P.R. / Baker, G.E.
History
DepositionJan 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: 2-methylcitrate dehydratase
D: 2-methylcitrate dehydratase
A: 2-methylcitrate dehydratase
B: 2-methylcitrate dehydratase
C: 2-methylcitrate dehydratase
F: 2-methylcitrate dehydratase


Theoretical massNumber of molelcules
Total (without water)322,5506
Polymers322,5506
Non-polymers00
Water00
1
E: 2-methylcitrate dehydratase
F: 2-methylcitrate dehydratase


Theoretical massNumber of molelcules
Total (without water)107,5172
Polymers107,5172
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-30 kcal/mol
Surface area24120 Å2
MethodPISA
2
D: 2-methylcitrate dehydratase
C: 2-methylcitrate dehydratase


Theoretical massNumber of molelcules
Total (without water)107,5172
Polymers107,5172
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-28 kcal/mol
Surface area24220 Å2
MethodPISA
3
A: 2-methylcitrate dehydratase
B: 2-methylcitrate dehydratase


Theoretical massNumber of molelcules
Total (without water)107,5172
Polymers107,5172
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-29 kcal/mol
Surface area28370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.662, 139.662, 513.484
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11E
21D
12E
22A
13E
23B
14E
24C
15E
25F
16D
26A
17D
27B
18D
28C
19D
29F
110A
210B
111A
211C
112A
212F
113B
213C
114B
214F
115C
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALEA11 - 48211 - 482
21VALVALDB11 - 48211 - 482
12TYRTYREA11 - 48111 - 481
22PHEPHEAC11 - 35811 - 358
13VALVALEA11 - 48211 - 482
23VALVALBD11 - 48211 - 482
14VALVALEA11 - 48211 - 482
24VALVALCE11 - 48211 - 482
15VALVALEA11 - 48211 - 482
25VALVALFF11 - 48211 - 482
16TYRTYRDB11 - 48111 - 481
26PHEPHEAC11 - 35811 - 358
17VALVALDB11 - 48211 - 482
27VALVALBD11 - 48211 - 482
18VALVALDB11 - 48211 - 482
28VALVALCE11 - 48211 - 482
19VALVALDB11 - 48211 - 482
29VALVALFF11 - 48211 - 482
110PHEPHEAC11 - 35811 - 358
210TYRTYRBD11 - 48111 - 481
111PHEPHEAC11 - 35811 - 358
211TYRTYRCE11 - 48111 - 481
112PHEPHEAC11 - 35811 - 358
212TYRTYRFF11 - 48111 - 481
113VALVALBD11 - 48211 - 482
213VALVALCE11 - 48211 - 482
114VALVALBD11 - 48211 - 482
214VALVALFF11 - 48211 - 482
115VALVALCE11 - 48211 - 482
215VALVALFF11 - 48211 - 482

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
2-methylcitrate dehydratase


Mass: 53758.270 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: prpD, AEV26_14870 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0L5RC52, UniProt: Q8Z903*PLUS, 2-methylcitrate dehydratase

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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: 2.99 Å3/Da / Density % sol: 58.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium fluoride 20% w/vPEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.532
11K, H, -L20.468
ReflectionResolution: 3.05→39.14 Å / Num. obs: 70843 / % possible obs: 99.5 % / Redundancy: 9 % / Net I/σ(I): 5.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 3.05→39.14 Å / Cor.coef. Fo:Fc: 0.798 / Cor.coef. Fo:Fc free: 0.758 / SU B: 9.6 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.074 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2387 3483 4.9 %RANDOM
Rwork0.21313 ---
obs0.21437 67359 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 8.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.83 Å20 Å20 Å2
2--4.83 Å20 Å2
3----9.65 Å2
Refinement stepCycle: 1 / Resolution: 3.05→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15106 0 0 0 15106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01915410
X-RAY DIFFRACTIONr_bond_other_d0.0070.0213757
X-RAY DIFFRACTIONr_angle_refined_deg1.4191.94520932
X-RAY DIFFRACTIONr_angle_other_deg1.231331425
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.11852122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.40223.577520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.447152093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9541573
X-RAY DIFFRACTIONr_chiral_restr0.0870.22368
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02117960
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023419
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9670.8898524
X-RAY DIFFRACTIONr_mcbond_other0.9670.8898523
X-RAY DIFFRACTIONr_mcangle_it1.6891.3310634
X-RAY DIFFRACTIONr_mcangle_other1.6881.3310635
X-RAY DIFFRACTIONr_scbond_it0.8470.9516886
X-RAY DIFFRACTIONr_scbond_other0.8470.9516887
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.4631.40510299
X-RAY DIFFRACTIONr_long_range_B_refined2.8896.92516900
X-RAY DIFFRACTIONr_long_range_B_other2.8886.92516901
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11E156040.06
12D156040.06
21E135890.09
22A135890.09
31E153980.06
32B153980.06
41E154530.07
42C154530.07
51E157090.06
52F157090.06
61D140660.09
62A140660.09
71D155950.06
72B155950.06
81D156610.07
82C156610.07
91D158400.06
92F158400.06
101A138470.09
102B138470.09
111A140370.09
112C140370.09
121A138950.09
122F138950.09
131B155220.06
132C155220.06
141B154880.06
142F154880.06
151C157720.06
152F157720.06
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 261 -
Rwork0.276 4954 -
obs--99.41 %

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