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- PDB-4e0b: 2.17 Angstrom resolution crystal structure of malate dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 4e0b
Title2.17 Angstrom resolution crystal structure of malate dehydrogenase from Vibrio vulnificus CMCP6
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / malate dehydrogenase / Type III Secretion System / virulence / pathogenesis / toxin / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / tricarboxylic acid cycle / carbohydrate metabolic process
Similarity search - Function
Malate dehydrogenase, type 1, bacterial / Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain ...Malate dehydrogenase, type 1, bacterial / Malate dehydrogenase, type 1 / Malate dehydrogenase, active site / Malate dehydrogenase active site signature. / L-2-Hydroxyisocaproate Dehydrogenase; Chain A, domain 2 / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / L-lactate/malate dehydrogenase / Lactate/malate dehydrogenase, N-terminal / Lactate/malate dehydrogenase, C-terminal / lactate/malate dehydrogenase, NAD binding domain / lactate/malate dehydrogenase, alpha/beta C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Malate dehydrogenase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsHalavaty, A.S. / Wawrzak, Z. / Onopriyenko, O. / Kwon, K. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 2.17 Angstrom resolution crystal structure of malate dehydrogenase from Vibrio vulnificus CMCP6
Authors: Halavaty, A.S. / Wawrzak, Z. / Onopriyenko, O. / Kwon, K. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMar 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malate dehydrogenase
B: Malate dehydrogenase
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,8678
Polymers130,6314
Non-polymers2364
Water12,773709
1
A: Malate dehydrogenase
B: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4334
Polymers65,3152
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-22 kcal/mol
Surface area23220 Å2
MethodPISA
2
C: Malate dehydrogenase
D: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4334
Polymers65,3152
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-23 kcal/mol
Surface area22980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.040, 80.760, 99.430
Angle α, β, γ (deg.)90.00, 109.42, 90.00
Int Tables number4
Space group name H-MP1211
DetailsChains A and B - asymmetric unit dimer Identical dimer can be generated by symmetry operation [-X,Y+1/2,-Z+(001)] for chain C and [-X,Y+1/2,-Z+(011)] for chain D

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Components

#1: Protein
Malate dehydrogenase


Mass: 32657.684 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: mdh, VV1_0673 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q8DEC2, malate dehydrogenase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 709 / 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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 295 K / pH: 7
Details: Protein: 3.3 mg/mL. Crystallization conditions: 30%PEG 8K, 0.2M Na Acetate , 0.1M Bis-Tris pH 7.0. , VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 12, 2012 / Details: BE-LENSES
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.17→30 Å / Num. obs: 62995 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.3 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 13.87
Reflection shellResolution: 2.17→2.21 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 2.19 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
mrbump/molrepmodel building
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
MRBUMP/MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HHP

3hhp


Resolution: 2.17→29.2 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 11.381 / SU ML: 0.131 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 3147 5 %RANDOM
Rwork0.163 ---
obs0.165 59311 99.8 %-
all-59311 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 34.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å2-0.74 Å2
2---0.64 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.17→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8875 0 16 709 9600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0229191
X-RAY DIFFRACTIONr_bond_other_d0.0010.025977
X-RAY DIFFRACTIONr_angle_refined_deg1.271.98712505
X-RAY DIFFRACTIONr_angle_other_deg0.796314806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.64551250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.10825.731342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.607151514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.7481535
X-RAY DIFFRACTIONr_chiral_restr0.0740.21499
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110461
X-RAY DIFFRACTIONr_gen_planes_other00.021642
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_it0.4871.56138
X-RAY DIFFRACTIONr_mcbond_other0.1091.52554
X-RAY DIFFRACTIONr_mcangle_it0.9129829
X-RAY DIFFRACTIONr_scbond_it1.62933053
X-RAY DIFFRACTIONr_scangle_it2.7194.52676
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.17→2.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 259 -
Rwork0.212 4319 -
obs--99.96 %
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)
11.45921.00731.15782.7041.1121.6062-0.0340.1291-0.0025-0.25050.05480.0586-0.11110.0934-0.02080.0845-0.0150.0250.09590.0130.02613.724450.3459-13.7948
21.01860.30550.1841.04580.25161.47550.068-0.047-0.15370.07760.0117-0.08830.14480.0362-0.07980.06560.0031-0.0160.03040.01630.06437.964534.1326-0.6706
31.9943-0.05060.41872.72250.35221.4322-0.0375-0.10.0703-00.0491-0.0192-0.0020.0419-0.01160.00110.0017-0.00010.07720.01590.015316.180660.515111.4613
41.85060.3293-0.29961.14890.05941.6821-0.03440.02760.1222-0.08060.0445-0.1157-0.14150.3088-0.01010.0357-0.0630.00330.15380.0070.082532.023871.11324.4196
51.98211.6753-0.41923.5138-0.55811.4418-0.1190.22810.0031-0.4240.2169-0.03970.21820.0003-0.09790.1789-0.067-0.0290.07890.00030.0248-26.390140.469329.9518
61.11740.5579-0.30861.3277-0.29581.51220.02060.04110.2179-0.00370.10180.1871-0.0831-0.0814-0.12250.0846-0.0040.0090.01340.0150.0943-24.039356.856544.0874
71.7582-0.7921-0.04512.52150.46110.8503-0.01360.0487-0.0349-0.0620.0587-0.13420.02310.0265-0.0450.0455-0.00540.02570.0251-0.01060.0301-35.89127.90854.815
81.6799-0.620.33841.9929-0.1051.766-0.1625-0.21710.02760.3460.153-0.40910.08650.21290.00960.13790.0865-0.06670.1228-0.04540.1785-49.79220.13340.855
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 115
2X-RAY DIFFRACTION2A116 - 309
3X-RAY DIFFRACTION3B0 - 91
4X-RAY DIFFRACTION4B92 - 309
5X-RAY DIFFRACTION5C0 - 117
6X-RAY DIFFRACTION6C118 - 309
7X-RAY DIFFRACTION7D0 - 115
8X-RAY DIFFRACTION8D116 - 309

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