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- PDB-5vfb: 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G f... -

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Basic information

Entry
Database: PDB / ID: 5vfb
Title1.36 Angstrom Resolution Crystal Structure of Malate Synthase G from Pseudomonas aeruginosa in Complex with Glycolic Acid.
ComponentsMalate synthase G
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Malate Synthase G / Glycolic Acid
Function / homology
Function and homology information


malate synthase / malate synthase activity / glyoxylate catabolic process / glyoxylate cycle / tricarboxylic acid cycle / magnesium ion binding / cytosol
Similarity search - Function
Malate synthase G / Malate synthase, domain III / Malate synthase, domain 3 / Malate synthase, N-terminal and TIM-barrel domains / Malate Synthase G; Chain: A; Domain 4 / Malate synthase, C-terminal superfamily / Malate synthase / Malate synthase superfamily / Malate synthase, TIM barrel domain / TIM Barrel ...Malate synthase G / Malate synthase, domain III / Malate synthase, domain 3 / Malate synthase, N-terminal and TIM-barrel domains / 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
GLYCOLIC ACID / NICKEL (II) ION / Malate synthase G
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G from Pseudomonas aeruginosa in Complex with Glycolic Acid.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Kiryukhina, O. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionApr 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)158,72018
Polymers158,0502
Non-polymers67016
Water40,4802247
1
A: Malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,3378
Polymers79,0251
Non-polymers3127
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,38310
Polymers79,0251
Non-polymers3589
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.385, 111.712, 96.954
Angle α, β, γ (deg.)90.00, 100.42, 90.00
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: 79025.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: glcB, PA0482 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q9I636, malate synthase

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Non-polymers , 5 types, 2263 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID / Glycolic acid


Mass: 76.051 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2247 / 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: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Protein: 14.6 mg/ml, 0.01M Tris HCl (pH 8.3); Screen: PACT (A7), 0.2M Sodium chloride, 0.1M Sodium acetate pH (5.0), 20% (w/v) PEG 6000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 28, 2017 / Details: C(111)
RadiationMonochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.36→30 Å / Num. obs: 280381 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.047 / Rsym value: 0.087 / Χ2: 1.003 / Net I/σ(I): 15.4
Reflection shellResolution: 1.36→1.38 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 13617 / CC1/2: 0.607 / Rpim(I) all: 0.426 / Rsym value: 0.715 / Χ2: 1.003 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S9Z

3s9z


Resolution: 1.36→29.62 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.697 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.054 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16782 13944 5 %RANDOM
Rwork0.14333 ---
obs0.14453 266396 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.977 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.13 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.36→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11050 0 24 2247 13321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01912122
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211270
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.95316536
X-RAY DIFFRACTIONr_angle_other_deg0.867326207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.92651620
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67624.724561
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.905152085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9941584
X-RAY DIFFRACTIONr_chiral_restr0.0930.21818
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.0214181
X-RAY DIFFRACTIONr_gen_planes_other0.0210.022427
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_it0.6640.7256240
X-RAY DIFFRACTIONr_mcbond_other0.6640.7256239
X-RAY DIFFRACTIONr_mcangle_it1.0941.0877940
X-RAY DIFFRACTIONr_mcangle_other1.0941.0877941
X-RAY DIFFRACTIONr_scbond_it1.1490.845882
X-RAY DIFFRACTIONr_scbond_other1.1490.845882
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7731.2128597
X-RAY DIFFRACTIONr_long_range_B_refined4.60511.07215067
X-RAY DIFFRACTIONr_long_range_B_other3.9979.41114173
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.361→1.396 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 971 -
Rwork0.232 18812 -
obs--94.8 %
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)
10.52940.1323-0.04340.19690.13240.46160.03620.04810.0016-0.0138-0.02570.0131-0.0507-0.0271-0.01050.0090.00560.00030.0188-0.00070.01099.51692.247414.3757
20.09260.0126-0.06870.0877-0.0630.5095-0.0053-0.02360.0105-0.00030.0136-0.03270.05090.0057-0.00840.0233-0.0049-0.00840.0142-0.00590.018219.16130.567645.7744
30.1148-0.03350.05590.06750.10920.39050.005-0.00720.01670.0140.0015-0.01480.0043-0.0157-0.00650.0243-0.006-0.00050.0099-0.00290.021816.43895.538440.6158
40.26090.119-0.16030.2859-0.06590.44770.0137-0.0257-0.04830.025-0.001-0.04720.07080.0581-0.01270.02270.0078-0.01710.0111-0.00220.022224.3862-15.808822.9465
50.1461-0.03030.08850.0943-0.12570.49060.0024-0.0422-0.00380.02340.03060.0143-0.0056-0.0361-0.0330.01420.00520.00510.01860.00320.0039-7.830241.890127.482
67.57922.07122.61161.126-0.37463.3982-0.0242-0.0342-0.0175-0.0286-0.0776-0.05340.093-0.030.10170.0129-0.02040.01120.06770.00040.022-29.132747.108536.5022
70.1255-0.03480.04170.1305-0.15160.3545-0.0073-0.01030.0020.02960.01460.0023-0.01120.0076-0.00730.01440.00130.00070.012100.0031-2.3943.741419.1264
80.9208-0.1328-0.40280.16850.03760.5284-0.05920.0732-0.0840.00390.03920.04670.1154-0.09180.020.0365-0.0264-0.00180.03560.0070.0209-20.176132.11744.3812
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 91
2X-RAY DIFFRACTION2A92 - 166
3X-RAY DIFFRACTION3A167 - 566
4X-RAY DIFFRACTION4A567 - 725
5X-RAY DIFFRACTION5B2 - 301
6X-RAY DIFFRACTION6B302 - 313
7X-RAY DIFFRACTION7B314 - 568
8X-RAY DIFFRACTION8B569 - 725

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