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- PDB-4e4g: Crystal structure of putative Methylmalonate-semialdehyde dehydro... -

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Basic information

Entry
Database: PDB / ID: 4e4g
TitleCrystal structure of putative Methylmalonate-semialdehyde dehydrogenase from Sinorhizobium meliloti 1021
ComponentsMethylmalonate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


methylmalonate-semialdehyde dehydrogenase (CoA-acylating) / methylmalonate-semialdehyde dehydrogenase (acylating, NAD) activity / nucleotide binding
Similarity search - Function
Methylmalonate-semialdehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal ...Methylmalonate-semialdehyde dehydrogenase / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
methylmalonate-semialdehyde dehydrogenase (CoA acylating)
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. ...Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Zenchek, W. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of putative Methylmalonate-semialdehyde dehydrogenase from Sinorhizobium meliloti 1021
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. ...Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Zenchek, W. / Love, J. / Fiser, A. / Khafizov, K. / Seidel, R. / Bonanno, J.B. / Almo, S.C.
History
DepositionMar 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Structure summary
Revision 1.2Aug 29, 2012Group: Derived calculations
Revision 1.3Sep 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
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
Revision 1.4Dec 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: Methylmalonate-semialdehyde dehydrogenase
B: Methylmalonate-semialdehyde dehydrogenase
C: Methylmalonate-semialdehyde dehydrogenase
D: Methylmalonate-semialdehyde dehydrogenase
E: Methylmalonate-semialdehyde dehydrogenase
F: Methylmalonate-semialdehyde dehydrogenase
G: Methylmalonate-semialdehyde dehydrogenase
H: Methylmalonate-semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)457,9508
Polymers457,9508
Non-polymers00
Water6,125340
1
A: Methylmalonate-semialdehyde dehydrogenase
B: Methylmalonate-semialdehyde dehydrogenase
C: Methylmalonate-semialdehyde dehydrogenase
D: Methylmalonate-semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)228,9754
Polymers228,9754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19750 Å2
ΔGint-76 kcal/mol
Surface area59410 Å2
MethodPISA
2
E: Methylmalonate-semialdehyde dehydrogenase
F: Methylmalonate-semialdehyde dehydrogenase
G: Methylmalonate-semialdehyde dehydrogenase
H: Methylmalonate-semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)228,9754
Polymers228,9754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19290 Å2
ΔGint-80 kcal/mol
Surface area59580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)197.442, 171.285, 159.690
Angle α, β, γ (deg.)90.000, 124.030, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11G-526-

HOH

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Components

#1: Protein
Methylmalonate-semialdehyde dehydrogenase


Mass: 57243.699 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: iolA, mmsA, R00726, SMc00781 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL
References: UniProt: Q92RW4, methylmalonate-semialdehyde dehydrogenase (CoA-acylating)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MgCl2, 0.1M MES:NaOH, pH 6.5, 30% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 100867 / % possible obs: 98.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.136 / Χ2: 0.968 / Net I/σ(I): 6.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-2.9550.60850500.779199.2
2.95-350.53450410.765199.3
3-3.065.10.45250280.764199.1
3.06-3.1250.37650340.787199.3
3.12-3.195.10.34150510.798199.4
3.19-3.275.10.29450870.813199.2
3.27-3.355.20.25450110.842199.4
3.35-3.445.20.20150620.848199.4
3.44-3.545.30.17450360.92199.3
3.54-3.655.30.15550760.959199.4
3.65-3.785.50.14250411.056199.2
3.78-3.945.40.13250491.057199.3
3.94-4.115.50.11750761.134199.1
4.11-4.335.50.11150281.104199.1
4.33-4.65.50.09450361.114198.9
4.6-4.965.40.0950321.144198.5
4.96-5.465.40.09650111.048198.2
5.46-6.245.70.10350471.101198.5
6.24-7.865.70.09150301.095198
7.86-505.50.06650411.115196.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.55 Å48.84 Å
Translation2.55 Å48.84 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T90

1t90


Resolution: 2.9→19.97 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.867 / WRfactor Rfree: 0.2481 / WRfactor Rwork: 0.1734 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7925 / SU B: 40.56 / SU ML: 0.357 / SU R Cruickshank DPI: 0.3494 / SU Rfree: 0.4552 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.455 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2692 4795 5 %RANDOM
Rwork0.188 ---
obs0.192 95962 98.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.39 Å2 / Biso mean: 43.1438 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.19 Å2
2---0.09 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29313 0 0 340 29653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01929935
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.97540571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68853880
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46123.9781272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.709154442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.27315200
X-RAY DIFFRACTIONr_chiral_restr0.1020.24464
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02122944
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 312 -
Rwork0.276 6563 -
all-6875 -
obs--99.21 %
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)
10.4877-0.3262-0.18021.17450.19730.3014-0.04380.0452-0.0503-0.19010.0699-0.20960.16630.0441-0.02610.19460.00830.06450.0342-0.04950.1118-48.2066-10.9155-6.7644
20.4965-0.2029-0.03760.9634-0.16320.48470.00330.01630.2036-0.22820.1205-0.3219-0.02020.0943-0.12380.1196-0.04530.11750.0522-0.06620.2441-43.573226.6671-5.5797
31.1073-0.60380.11620.78090.25120.5832-0.0913-0.144-0.09610.10440.08850.10960.1309-0.07110.00280.056-0.00240.02230.0310.02210.0362-81.24466.038618.4181
40.8866-0.28280.20050.95590.01530.7869-0.1382-0.35220.13750.33910.2168-0.27090.09080.1807-0.07860.14450.1289-0.10740.2654-0.13160.1108-48.454212.317936.4948
50.6-0.01790.22830.72050.20560.7210.04920.4784-0.1107-0.01850.0587-0.17280.24550.4107-0.1080.13990.168-0.03710.5626-0.14110.0808-94.02968.312659.9833
60.3458-0.07360.18040.8841-0.26150.9446-0.04840.37280.1992-0.18370.0279-0.0843-0.06360.52650.02050.0889-0.1233-0.00850.58410.18110.1821-87.678645.647460.0349
71.7525-0.46111.10770.5866-0.11411.18630.0258-0.03860.03070.0907-0.03880.10430.1548-0.1450.0130.088-0.03630.04410.0308-0.00120.0569-126.579527.433984.6501
81.318-0.16750.7370.4801-0.13121.022-0.04760.02160.23890.1638-0.0205-0.10210.01110.22150.06810.11850.0065-0.01960.0757-0.0160.0722-93.311432.5094102.6968
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 486
2X-RAY DIFFRACTION2B0 - 485
3X-RAY DIFFRACTION3C-1 - 484
4X-RAY DIFFRACTION4D-1 - 486
5X-RAY DIFFRACTION5E0 - 485
6X-RAY DIFFRACTION6F1 - 484
7X-RAY DIFFRACTION7G-2 - 482
8X-RAY DIFFRACTION8H1 - 485

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