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- PDB-6kcx: Crystal structure of citrate complex of alpha-glucuronidase (TM07... -

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Basic information

Entry
Database: PDB / ID: 6kcx
TitleCrystal structure of citrate complex of alpha-glucuronidase (TM0752)from Thermotoga maritima
ComponentsAlpha-glucosidase, putative
KeywordsHYDROLASE / Glycosyl hydrolase / Carbohydrate metabolism / Alpha-glucuronidase / Citrate complex / NAD(P) binding Rossman fold domain-like / LDH C-terminal domain-like / Cobalt bound
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / nucleotide binding / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 4 / Glycosyl hydrolase, family 4, C-terminal / Family 4 glycosyl hydrolase / Family 4 glycosyl hydrolase C-terminal domain / Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
CITRIC ACID / : / IMIDAZOLE / ISOPROPYL ALCOHOL / Alpha-glucosidase, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.933 Å
AuthorsManoj, N. / Mohapatra, B.S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Structure of an alpha-glucuronidase in complex with Co2+and citrate provides insights into the mechanism and substrate recognition in the family 4 glycosyl hydrolases.
Authors: Mohapatra, S.B. / Manoj, N.
History
DepositionJun 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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_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.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.value / _struct_conn.pdbx_dist_value / _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

Downloads & links

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Assembly

Deposited unit
A: Alpha-glucosidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4686
Polymers56,8961
Non-polymers5725
Water6,864381
1
A: Alpha-glucosidase, putative
hetero molecules

A: Alpha-glucosidase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,93612
Polymers113,7922
Non-polymers1,14510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
Buried area2970 Å2
ΔGint-15 kcal/mol
Surface area35120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.420, 80.410, 89.050
Angle α, β, γ (deg.)90.000, 102.100, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alpha-glucosidase, putative


Mass: 56895.852 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0752 / Plasmid: pMH
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9WZL1

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Non-polymers , 5 types, 386 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12 % PEG 3350, 0.2 M trilithium citrate, 0.1 M imidazole, pH 5.8, 2-propanol
PH range: 5.8-6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 1, 2013
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.93→43.54 Å / Num. obs: 38318 / % possible obs: 98.6 % / Redundancy: 6.1 % / Biso Wilson estimate: 16.23 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.033 / Rrim(I) all: 0.083 / Net I/σ(I): 18.2 / Num. measured all: 232326 / Scaling rejects: 29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.93-1.975.50.3621214222210.8890.1660.3994.880.6
8.83-43.545.90.03225274260.9990.0140.03543.499

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.93 Å40.2 Å
Translation6.99 Å40.2 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1-2575refinement
MOSFLM7.2.1data reduction
Aimless0.1.26data scaling
PHASER2.5.5phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VJT

1vjt


Resolution: 1.933→40.205 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 16.25
RfactorNum. reflection% reflectionSelection details
Rfree0.1843 1916 5 %Random selection
Rwork0.1411 ---
obs0.1432 38312 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.8 Å2 / Biso mean: 22.3266 Å2 / Biso min: 7.2 Å2
Refinement stepCycle: final / Resolution: 1.933→40.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3810 0 59 381 4250
Biso mean--30.5 25.51 -
Num. residues----470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053967
X-RAY DIFFRACTIONf_angle_d0.7345392
X-RAY DIFFRACTIONf_chiral_restr0.046566
X-RAY DIFFRACTIONf_plane_restr0.005704
X-RAY DIFFRACTIONf_dihedral_angle_d12.6222361
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 (%)
1.9329-1.98130.26191290.17582447257694
1.9813-2.03480.1931270.152726292756100
2.0348-2.09470.19331140.14526042718100
2.0947-2.16230.1571390.135625842723100
2.1623-2.23960.20051550.129525842739100
2.2396-2.32930.17081330.124626002733100
2.3293-2.43530.17461310.134226012732100
2.4353-2.56360.18581360.137726082744100
2.5636-2.72420.2031370.143826352772100
2.7242-2.93450.2181290.157125872716100
2.9345-3.22970.21031390.161626312770100
3.2297-3.69680.1751600.149325972757100
3.6968-4.65640.1611440.113626222766100
4.6564-40.21370.16041430.143326672810100
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)
11.1554-0.04360.26280.91380.0251.28340.00130.25670.016-0.3052-0.00890.0607-0.132-0.09850.00070.25110.0267-0.00230.23380.00510.11713.95695.779789.6546
20.24130.10680.19670.5887-0.37750.87670.05190.1075-0.0837-0.1627-0.0582-0.05930.04730.07260.02370.15310.02630.02070.1545-0.02990.16512.8328-8.0888108.7422
31.2467-0.2465-0.5230.6863-0.14371.10960.05440.0931-0.0062-0.14810.00170.0384-0.0718-0.0319-0.05630.14820.0003-0.01130.0975-0.00390.11413.53116.5047109.756
40.5847-0.04840.13221.15320.13680.69-0.01330.0141-0.0927-0.0470.03190.26350.0051-0.1587-0.02130.0895-0.0047-0.01210.14230.00720.1653-11.4213-4.6749120.1518
50.1422-0.0843-0.11940.5203-1.14413.2371-0.19080.1609-0.1148-0.3435-0.0516-0.05160.2727-0.26410.15260.2899-0.0239-0.03730.2339-0.07490.210.1721-13.487993.1467
60.2621-0.029-0.19610.4045-0.12671.22240.02810.06910.0218-0.1057-0.01980.0765-0.1496-0.2394-0.00340.14350.0417-0.01170.14840.00490.1382-2.81529.843109.4194
70.27650.15090.0560.7601-0.1210.7650.03030.0611-0.0591-0.0748-0.0446-0.10780.07520.10290.00810.10740.02390.00540.1349-0.0140.135119.1299-8.7065119.5097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 82 )A0 - 82
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 149 )A83 - 149
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 193 )A150 - 193
4X-RAY DIFFRACTION4chain 'A' and (resid 194 through 297 )A194 - 297
5X-RAY DIFFRACTION5chain 'A' and (resid 298 through 322 )A298 - 322
6X-RAY DIFFRACTION6chain 'A' and (resid 323 through 408 )A323 - 408
7X-RAY DIFFRACTION7chain 'A' and (resid 409 through 469 )A409 - 469

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