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- PDB-4ex4: The Structure of GlcB from Mycobacterium leprae -

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Basic information

Entry
Database: PDB / ID: 4ex4
TitleThe Structure of GlcB from Mycobacterium leprae
ComponentsMalate synthase G
KeywordsTRANSFERASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease / Malate synthase / Mycobacterium leprae / NIAID / National Institute of Allergy and Infectious Diseases / Synthase
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 - maily-beta sub-domain / Malate synthase G - maily-beta sub-domain / Malate synthase G / Malate synthase, domain III / Malate synthase, domain 3 / Malate Synthase G; Chain: A; Domain 4 / Malate synthase / Malate synthase superfamily / Malate synthase, TIM barrel domain ...: / Malate synthase G - maily-beta sub-domain / Malate synthase G - maily-beta sub-domain / Malate synthase G / Malate synthase, domain III / Malate synthase, domain 3 / Malate Synthase G; Chain: A; Domain 4 / Malate synthase / Malate synthase superfamily / Malate synthase, TIM barrel domain / Beta Complex / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMycobacterium leprae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: The Structure of GlcB from Mycobacterium leprae
Authors: Clifton, M.C. / Fox III, D. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionApr 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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.value / _struct_conn.pdbx_dist_value / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)161,2619
Polymers161,0532
Non-polymers2087
Water15,601866
1
A: Malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6625
Polymers80,5271
Non-polymers1354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Malate synthase G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,6004
Polymers80,5271
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.610, 59.740, 118.460
Angle α, β, γ (deg.)90.00, 100.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Malate synthase G


Mass: 80526.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium leprae (bacteria) / Strain: Br4923 / Gene: glcB, ML2069, MLBr02069, MLCB1788.27 / Production host: Escherichia coli (E. coli) / References: UniProt: B8ZSN3, malate synthase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 866 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE AT POSITION 595 IS CONFIRMED TO BE LYS

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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: 2.3 Å3/Da / Density % sol: 46.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MyleA18344aA1 PW34800 19.28mg/ml, 100mM HEPES pH7.5, 20%w/v PEG4000, 10% Isopropanol. Cryoprotection 20% ethylene glycol. , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 85731 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.24
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.150.433.17199.1
2.15-2.210.3843.83199.7
2.21-2.280.3494.21199.7
2.28-2.350.3054.73199.6
2.35-2.420.2695.38199.7
2.42-2.510.2356.06199.8
2.51-2.60.2026.76199.7
2.6-2.710.1777.52199.9
2.71-2.830.1568.36199.9
2.83-2.970.12410.01199.9
2.97-3.130.10511.531100
3.13-3.320.07915.16199.9
3.32-3.550.06119.67199.9
3.55-3.830.04925.18199.8
3.83-4.20.04427.78199.9
4.2-4.70.03732.36199.6
4.7-5.420.03829.79199.7
5.42-6.640.0523.65199.9
6.64-9.390.03334.01199.3
9.390.02251.58195.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N8I

1n8i


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.904 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 8.877 / SU ML: 0.127 / SU R Cruickshank DPI: 0.2205 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23423 4292 5 %RANDOM
Rwork0.18078 ---
obs0.18341 81426 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.128 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20.05 Å2
2--0.04 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10599 0 10 866 11475
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01910842
X-RAY DIFFRACTIONr_bond_other_d0.0010.027053
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.95314773
X-RAY DIFFRACTIONr_angle_other_deg0.955317228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32651408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.23124.525484
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.535151699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9131571
X-RAY DIFFRACTIONr_chiral_restr0.0850.21703
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112319
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022148
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 302 -
Rwork0.214 5731 -
obs--98.95 %
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)
11.3610.26210.11450.4753-0.00220.47460.0531-0.1352-0.14620.0469-0.0146-0.06510.03730.0083-0.03840.04070.0092-0.01920.01910.01130.065747.463212.526143.6458
21.4015-0.412-0.02790.46380.25660.22690.10990.5836-0.1098-0.077-0.17110.0728-0.03960.0270.06120.07020.0541-0.02540.2973-0.0410.048541.690816.47159.122
31.16180.14540.22460.1334-0.00770.19470.04540.0527-0.16930.0111-0.0073-0.0104-0.00190.0266-0.03810.06090.0142-0.00510.0218-0.01190.104142.209110.911335.646
41.0978-0.08410.35990.04460.05961.0728-0.01410.2896-0.0012-0.02920.0068-0.0449-0.12130.11330.00730.0572-0.00380.03370.1273-0.01440.085958.091619.451723.9491
50.88730.2321-0.04141.5266-0.10350.1659-0.04890.00120.1358-0.09580.0479-0.0127-0.0509-0.00130.0010.10540.0063-0.00710.0029-0.00410.088344.516438.268139.1275
61.5046-0.35410.01670.6432-0.06360.52350.07240.2749-0.1522-0.1312-0.0177-0.07430.0307-0.0335-0.05470.08440.01970.00610.0903-0.03020.04682.89034.155213.3184
70.4526-0.02570.01870.25430.17270.86920.0605-0.09780.11510.0478-0.00480.0136-0.108-0.0459-0.05570.07880.01250.03210.0452-0.01620.063-4.164220.75948.3527
80.736-0.1049-0.09870.229-0.03240.27810.03930.0342-0.0032-0.0045-0.0063-0.0134-0.0144-0.0554-0.03290.06770.02230.00730.0480.00950.0645-2.165111.551328.7707
91.04460.19340.33290.40860.18620.79790.0759-0.0450.12610.0757-0.01560.0624-0.1032-0.0915-0.06030.07420.04950.04480.06590.01540.0862-15.40522.351338.2442
101.0169-0.26810.46961.12-0.15210.48110.0490.09970.1549-0.00080.01-0.0545-0.1713-0.0673-0.0590.16140.0820.08820.06090.07590.1031-2.20134.147515.5218
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 132
2X-RAY DIFFRACTION2A133 - 285
3X-RAY DIFFRACTION3A286 - 484
4X-RAY DIFFRACTION4A485 - 592
5X-RAY DIFFRACTION5A593 - 729
6X-RAY DIFFRACTION6B3 - 68
7X-RAY DIFFRACTION7B69 - 264
8X-RAY DIFFRACTION8B265 - 524
9X-RAY DIFFRACTION9B525 - 593
10X-RAY DIFFRACTION10B594 - 729

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