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- PDB-6axe: Crystal structure of a malate synthase G from Mycobacterium marin... -

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Basic information

Entry
Database: PDB / ID: 6axe
TitleCrystal structure of a malate synthase G from Mycobacterium marinum bound to acetyl CoA
ComponentsMalate synthase G
KeywordsHYDROLASE / NIAID / structural genomics / GlcB / coenzyme A / cofactor / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


malate synthase / malate synthase activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding / cytoplasm
Similarity search - Function
Malate synthase G / Malate synthase, domain III / Malate synthase, domain 3 / Malate Synthase G; Chain: A; Domain 4 / Malate synthase, C-terminal superfamily / Malate synthase / Malate synthase superfamily / Malate synthase, TIM barrel domain / TIM Barrel / Alpha-Beta Barrel ...Malate synthase G / Malate synthase, domain III / Malate synthase, domain 3 / Malate Synthase G; Chain: A; Domain 4 / Malate synthase, C-terminal superfamily / Malate synthase / Malate synthase superfamily / Malate synthase, TIM barrel domain / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / ACETATE ION / Malate synthase G
Similarity search - Component
Biological speciesMycobacterium marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a malate synthase G from Mycobacterium marinum bound to acetyl CoA
Authors: Edwards, T.E. / Dranow, D.M. / Lorimer, D.D. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionSep 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Malate synthase G
B: Malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,9808
Polymers161,1912
Non-polymers1,7896
Water34,0841892
1
A: Malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4894
Polymers80,5961
Non-polymers8933
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4924
Polymers80,5961
Non-polymers8963
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.600, 86.980, 124.130
Angle α, β, γ (deg.)90.000, 98.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Malate synthase G


Mass: 80595.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (strain ATCC BAA-535 / M) (bacteria)
Strain: ATCC BAA-535 / M / Gene: glcB, MMAR_2713 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HSY2, malate synthase

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Non-polymers , 5 types, 1898 molecules

#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1892 / 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: 2.6 Å3/Da / Density % sol: 52.76 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: MymaA.18344.a.B1.PS38275 at 23.7 mg/mL with 2 mM acetyl coenzyme A against JCSG+ screen condition H10 0.2 M ammonium acetate, 0.1 M BisTris pH 5.5, 25% PEG 3350 supplemented with 15% EG as ...Details: MymaA.18344.a.B1.PS38275 at 23.7 mg/mL with 2 mM acetyl coenzyme A against JCSG+ screen condition H10 0.2 M ammonium acetate, 0.1 M BisTris pH 5.5, 25% PEG 3350 supplemented with 15% EG as cryo-protectant, crystal tracking ID 292651h10, unique puck ID ltv3-10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.6→38.734 Å / Num. obs: 214046 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.994 % / Biso Wilson estimate: 20.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.057 / Χ2: 1.066 / Net I/σ(I): 14.33 / Num. measured all: 854923 / Scaling rejects: 126
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.643.0130.4522.09141540.8510.5488.1
1.64-1.693.4580.3962.74151800.9020.4797.4
1.69-1.743.8520.3263.66150070.9420.37998.6
1.74-1.794.2160.2664.87146320.9670.30599.2
1.79-1.854.2210.2046.27142220.9790.23499.3
1.85-1.914.2120.1647.72137780.9850.18899.3
1.91-1.984.2020.1279.92132760.990.14699.4
1.98-2.074.1860.10312.25128320.9920.11899.4
2.07-2.164.1610.08414.79122540.9940.09699.5
2.16-2.264.1460.07217.2117240.9950.08299.2
2.26-2.394.1240.06319.12112170.9960.07299.5
2.39-2.534.10.05621.45105650.9960.06499.3
2.53-2.74.080.04923.6999440.9970.05799.4
2.7-2.924.0470.04525.792860.9970.05299.6
2.92-3.24.0430.04227.8985510.9970.04899.5
3.2-3.584.0150.03829.5977560.9980.04499.7
3.58-4.134.0540.03530.9968570.9980.0499.6
4.13-5.064.0730.03231.8358110.9980.03699.8
5.06-7.164.0930.02831.7345320.9990.03399.7
7.16-38.7343.9120.02531.5724680.9980.02996.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3s9z

3s9z


Resolution: 1.6→38.734 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.91
RfactorNum. reflection% reflection
Rfree0.1739 1995 0.93 %
Rwork0.1522 --
obs0.1524 213968 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 89.96 Å2 / Biso mean: 29.5546 Å2 / Biso min: 13.11 Å2
Refinement stepCycle: final / Resolution: 1.6→38.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11021 0 112 1903 13036
Biso mean--42.41 39.72 -
Num. residues----1453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611528
X-RAY DIFFRACTIONf_angle_d0.81415740
X-RAY DIFFRACTIONf_chiral_restr0.0521805
X-RAY DIFFRACTIONf_plane_restr0.0052065
X-RAY DIFFRACTIONf_dihedral_angle_d16.2736928
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.640.27721290.2409134751360488
1.64-1.68430.24161420.218148691501197
1.6843-1.73390.22231410.1961150941523599
1.7339-1.78990.22031510.1869151911534299
1.7899-1.85380.20931520.1788152591541199
1.8538-1.92810.19291750.17152491542499
1.9281-2.01580.1941240.1673152741539899
2.0158-2.12210.18271350.1635152801541599
2.1221-2.2550.21281540.1596152811543599
2.255-2.42910.20341420.159152611540399
2.4291-2.67350.16881420.1552153121545499
2.6735-3.06020.15881300.14841539715527100
3.0602-3.8550.15111340.13731543515569100
3.855-38.74560.14091440.1265155961574099
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)
10.7169-0.2195-0.15682.5841.60292.10420.14870.1543-0.0838-0.1052-0.0777-0.40410.17870.2409-0.1050.17370.08660.02940.2530.0490.255626.8657-8.639450.0548
20.65110.15930.10370.390.04130.32110.0481-0.00260.02140.0131-0.05020.03180.02010.01640.00290.21870.00440.00090.15520.01830.188-3.8529-0.157753.7572
31.9316-0.58610.89780.8895-0.26961.05320.01760.0233-0.0582-0.0622-0.03460.21330.1045-0.15490.00470.1853-0.0084-0.00550.1448-0.02820.178-19.781-3.049138.9301
41.8812-0.46381.17540.7305-0.48311.21260.15110.1084-0.1781-0.127-0.0721-0.05460.26830.13-0.080.24740.06940.01240.1625-0.02040.17879.107-12.372742.0399
50.60470.0370.25490.7096-0.10150.74290.04520.0039-0.0082-0.0131-0.06070.01240.04110.01760.01730.14750.00640.00950.11770.00790.15716.21131.430458.5576
61.93220.5049-0.59341.2834-0.52222.42110.0724-0.047-0.30980.1154-0.049-0.01040.48170.04840.00430.27770.0154-0.04880.13480.04770.213912.8314-18.556171.7318
71.4076-0.73110.7481.1024-0.32081.14320.0713-0.1075-0.22230.0016-0.00290.12430.1559-0.1436-0.01970.145-0.0220.01760.19780.0310.175329.729727.10194.574
81.25310.25170.39981.49670.28961.8202-0.0361-0.18360.2521-0.0264-0.06950.221-0.101-0.2130.0620.13450.0235-0.02960.203-0.0460.237311.915363.33-15.7345
91.0719-0.52910.87361.0668-0.62190.98260.0364-0.1992-0.2086-0.02910.07230.26480.0747-0.2666-0.1260.1305-0.02150.00220.25780.01870.204316.296231.8979-1.3548
101.3753-0.13131.23850.93120.3881.79220.02990.02540.0734-0.0751-0.128-0.0189-0.0020.00280.05860.16910.00120.01030.21380.04310.21234.93534.1646-0.0222
111.2324-0.93231.0131.0372-0.44130.9133-0.0446-0.00550.22450.029-0.1177-0.2457-0.0428-0.00520.16340.1623-0.02680.00920.21560.04260.241935.92349.07920.4097
121.3363-0.45270.45721.93580.40061.6493-0.1759-0.30280.12770.31280.12730.1215-0.1883-0.41650.05220.26940.07450.01440.36460.00280.168126.559543.181724.4774
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 71 )A0 - 71
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 179 )A72 - 179
3X-RAY DIFFRACTION3chain 'A' and (resid 180 through 280 )A180 - 280
4X-RAY DIFFRACTION4chain 'A' and (resid 281 through 380 )A281 - 380
5X-RAY DIFFRACTION5chain 'A' and (resid 381 through 658 )A381 - 658
6X-RAY DIFFRACTION6chain 'A' and (resid 659 through 730 )A659 - 730
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 133 )B2 - 133
8X-RAY DIFFRACTION8chain 'B' and (resid 134 through 262 )B134 - 262
9X-RAY DIFFRACTION9chain 'B' and (resid 263 through 424 )B263 - 424
10X-RAY DIFFRACTION10chain 'B' and (resid 425 through 474 )B425 - 474
11X-RAY DIFFRACTION11chain 'B' and (resid 475 through 594 )B475 - 594
12X-RAY DIFFRACTION12chain 'B' and (resid 595 through 729 )B595 - 729

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