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- PDB-6aoo: 2.15 Angstrom Resolution Crystal Structure of Malate Dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 6aoo
Title2.15 Angstrom Resolution Crystal Structure of Malate Dehydrogenase from Haemophilus influenzae
ComponentsMalate dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Malate Dehydrogenase
Function / homology
Function and homology information


malate dehydrogenase / L-malate dehydrogenase (NAD+) activity / malate metabolic process / tricarboxylic acid cycle / cytoplasm
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
Malate dehydrogenase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMinasov, G. / Wawrzak, Z. / Skarina, T. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Microbiol Resour Announc / Year: 2025
Title: Structural genomics of bacterial drug targets: Application of a high-throughput pipeline to solve 58 protein structures from pathogenic and related bacteria.
Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / ...Authors: Inniss, N.L. / Minasov, G. / Chang, C. / Tan, K. / Kim, Y. / Maltseva, N. / Stogios, P. / Filippova, E. / Michalska, K. / Osipiuk, J. / Jaroszewki, L. / Godzik, A. / Savchenko, A. / Joachimiak, A. / Anderson, W.F. / Satchell, K.J.F.
History
DepositionAug 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 18, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2138
Polymers70,6372
Non-polymers5766
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, 3HHP
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-107 kcal/mol
Surface area25370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.688, 94.119, 73.215
Angle α, β, γ (deg.)90.00, 121.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Malate dehydrogenase


Mass: 35318.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: mdh, HI_1210 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P44427, malate dehydrogenase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.09 Å3/Da / Density % sol: 41.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20.0 mg/mL protein in 0.3 M sodium chloride, 0.01 M HEPES, pH 7.5, screen: 0.1 M lithium sulfate, 0.1 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 20% w/v PEG3350, 0.25 mM D-Malic acid, cryoprotectant: paratone

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07822 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 23, 2017 / Details: Si(111)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07822 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 33055 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.039 / Rsym value: 0.122 / Χ2: 1.026 / Net I/σ(I): 18.5
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1664 / CC1/2: 0.876 / Rpim(I) all: 0.229 / Rsym value: 0.749 / Χ2: 1.022 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3HHP

3hhp


Resolution: 2.15→29.68 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / SU B: 15.399 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.211 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23732 1660 5 %RANDOM
Rwork0.18236 ---
obs0.18516 31307 97.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.215 Å2
Baniso -1Baniso -2Baniso -3
1-5.85 Å20 Å22.49 Å2
2---3.33 Å20 Å2
3----3.17 Å2
Refinement stepCycle: 1 / Resolution: 2.15→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4662 0 30 359 5051
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194754
X-RAY DIFFRACTIONr_bond_other_d0.0010.024633
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9936459
X-RAY DIFFRACTIONr_angle_other_deg0.879310738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.1925630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.65625.146171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.84415797
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.181523
X-RAY DIFFRACTIONr_chiral_restr0.0780.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.0215272
X-RAY DIFFRACTIONr_gen_planes_other0.020.02855
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_it1.9033.4972528
X-RAY DIFFRACTIONr_mcbond_other1.93.4962527
X-RAY DIFFRACTIONr_mcangle_it2.9635.2363156
X-RAY DIFFRACTIONr_mcangle_other2.9635.2373157
X-RAY DIFFRACTIONr_scbond_it2.0143.7542225
X-RAY DIFFRACTIONr_scbond_other2.0013.7312201
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2285.4783267
X-RAY DIFFRACTIONr_long_range_B_refined6.70444.4135393
X-RAY DIFFRACTIONr_long_range_B_other6.63743.95316
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 121 -
Rwork0.281 2339 -
obs--99.15 %
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)
11.56150.42720.19820.9297-1.27782.25050.00550.0725-0.0466-0.1233-0.0441-0.00190.1780.07230.03860.0515-0.0019-0.0650.1487-0.00410.129320.05119.673843.5549
21.2781-1.6293-2.62082.14753.26415.4707-0.10870.1162-0.00880.2037-0.1008-0.1310.1651-0.25710.20950.12850.0045-0.1170.19070.01610.393921.472420.189367.1716
30.76820.3828-0.16030.9623-0.11210.3216-0.04-0.16250.02740.06390.045-0.05450.00750.1035-0.0050.05130.0162-0.07450.1673-0.00350.114734.795616.420456.9714
46.1994-5.5728-3.28638.54074.65123.8162-0.1091-0.0725-0.05040.1723-0.10190.19340.08780.03660.2110.0307-0.0098-0.02950.05460.00190.058329.063818.442348.5358
51.4775-0.0442-0.2721.24050.25350.5484-0.1698-0.2729-0.19450.03540.0168-0.273-0.02740.27690.1530.06550.0424-0.05160.22820.06590.205141.80989.568658.6378
61.4867-1.2080.79631.7007-0.44221.2796-0.01580.01030.0560.02380.0089-0.1388-0.18250.06740.00680.08290.0031-0.08170.1578-0.00570.162823.272937.352444.0233
70.38861.4079-0.46147.07080.45422.84310.01770.03680.02090.07090.2834-0.1788-0.0120.1053-0.3010.0226-0.0351-0.05920.14740.06710.2001-2.86130.287343.6297
80.34320.11980.23591.90360.57910.44410.0560.0415-0.0265-0.1232-0.04060.1171-0.032-0.138-0.01550.06910.0375-0.08960.17560.03110.18019.083229.861529.1603
90.66761.2742-1.75267.0195-2.92464.68730.00510.23960.03450.18860.1258-0.0951-0.0164-0.6077-0.13080.0357-0.0225-0.04920.1652-0.00160.112616.465827.407635.9512
100.80930.65370.13512.04040.37512.01570.0570.14820.0228-0.1695-0.03520.1523-0.1891-0.1248-0.02190.07510.0383-0.07620.11530.02040.16357.79736.740922.6652
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 81
2X-RAY DIFFRACTION2A82 - 89
3X-RAY DIFFRACTION3A90 - 218
4X-RAY DIFFRACTION4A219 - 239
5X-RAY DIFFRACTION5A240 - 311
6X-RAY DIFFRACTION6B-7 - 79
7X-RAY DIFFRACTION7B80 - 93
8X-RAY DIFFRACTION8B94 - 218
9X-RAY DIFFRACTION9B219 - 238
10X-RAY DIFFRACTION10B239 - 311

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