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- PDB-5ulv: Malate dehydrogenase from Methylobacterium extorquens -

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Basic information

Entry
Database: PDB / ID: 5ulv
TitleMalate dehydrogenase from Methylobacterium extorquens
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / malate / dehydrogenase / NAD
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / lactate metabolic process / L-lactate dehydrogenase activity / pyruvate metabolic process / tricarboxylic acid cycle
Similarity search - Function
Malate dehydrogenase, type 3 / 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 ...Malate dehydrogenase, type 3 / 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
Malate dehydrogenase / Malate dehydrogenase
Similarity search - Component
Biological speciesMethylobacterium extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsGonzalez, J.M.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Conformational changes on substrate binding revealed by structures of Methylobacterium extorquens malate dehydrogenase.
Authors: Gonzalez, J.M. / Marti-Arbona, R. / Chen, J.C.H. / Broom-Peltz, B. / Unkefer, C.J.
History
DepositionJan 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2017Provider: repository / Type: Initial release
SupersessionAug 23, 2017ID: 4ROR
Revision 1.1Aug 23, 2017Group: Advisory / Data collection / Category: diffrn_detector / pdbx_database_PDB_obs_spr / Item: _diffrn_detector.detector
Revision 1.2Nov 14, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_special_symmetry
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Nov 21, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Oct 4, 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
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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7623
Polymers33,6821
Non-polymers802
Water6,377354
1
A: Malate dehydrogenase
hetero molecules

A: Malate dehydrogenase
hetero molecules

A: Malate dehydrogenase
hetero molecules

A: Malate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,04712
Polymers134,7274
Non-polymers3218
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
crystal symmetry operation9_554-x,-x+y,-z-1/31
crystal symmetry operation12_544x,x-y-1,-z-1/31
Buried area14790 Å2
ΔGint-107 kcal/mol
Surface area41810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.995, 108.995, 104.659
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-676-

HOH

21A-818-

HOH

31A-851-

HOH

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Components

#1: Protein Malate dehydrogenase


Mass: 33681.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium extorquens (bacteria) / Gene: mdh / Production host: Escherichia coli (E. coli)
References: UniProt: B7KVX2, UniProt: Q84FY8*PLUS, malate dehydrogenase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25-28% PEG400, 180-220mM CaCl2, 0.1M Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127092 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127092 Å / Relative weight: 1
ReflectionResolution: 1.66→37.75 Å / Num. obs: 44052 / % possible obs: 99.6 % / Redundancy: 11.2 % / Net I/σ(I): 14.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3gvh

3gvh


Resolution: 1.66→37.75 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.318 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.073 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16765 2191 5 %RANDOM
Rwork0.1395 ---
obs0.14084 41822 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.927 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.16 Å20 Å2
2--0.32 Å2-0 Å2
3----1.04 Å2
Refinement stepCycle: 1 / Resolution: 1.66→37.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2323 0 2 354 2679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192470
X-RAY DIFFRACTIONr_bond_other_d0.0020.022399
X-RAY DIFFRACTIONr_angle_refined_deg1.9091.9743374
X-RAY DIFFRACTIONr_angle_other_deg1.06935540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8175345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42725.21394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04715409
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5461510
X-RAY DIFFRACTIONr_chiral_restr0.1160.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022880
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02510
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_it2.0972.0041323
X-RAY DIFFRACTIONr_mcbond_other2.09721322
X-RAY DIFFRACTIONr_mcangle_it3.0552.9911669
X-RAY DIFFRACTIONr_mcangle_other3.0552.9951670
X-RAY DIFFRACTIONr_scbond_it2.9192.2191147
X-RAY DIFFRACTIONr_scbond_other2.9182.2221148
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5183.2161700
X-RAY DIFFRACTIONr_long_range_B_refined6.68817.3213149
X-RAY DIFFRACTIONr_long_range_B_other6.21816.3922908
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.655→1.698 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 176 -
Rwork0.203 2872 -
obs--94.81 %

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