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- PDB-6vzz: Crystal structure of glucokinase from Balamuthia mandrillaris in ... -

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Basic information

Entry
Database: PDB / ID: 6vzz
TitleCrystal structure of glucokinase from Balamuthia mandrillaris in complex with glucose
ComponentsBamaA.19900.a
KeywordsTRANSFERASE / SSGCID / Glucokinase / Balamuthia mandrillaris Lepto ID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologybeta-D-glucopyranose
Function and homology information
Biological speciesBalamuthia mandrillaris (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Antimicrob.Agents Chemother. / Year: 2022
Title: Characterization of Glucokinases from Pathogenic Free-Living Amoebae.
Authors: Milanes, J.E. / Suryadi, J. / Monaghan, N.P. / Harding, E.M. / Morris, C.S. / Rozema, S.D. / Khalifa, M.M. / Golden, J.E. / Phan, I.Q. / Zigweid, R. / Abendroth, J. / Rice, C.A. / McCord, H. ...Authors: Milanes, J.E. / Suryadi, J. / Monaghan, N.P. / Harding, E.M. / Morris, C.S. / Rozema, S.D. / Khalifa, M.M. / Golden, J.E. / Phan, I.Q. / Zigweid, R. / Abendroth, J. / Rice, C.A. / McCord, H.T. / Wilson, S. / Fenwick, M.K. / Morris, J.C.
History
DepositionFeb 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jun 15, 2022Group: Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BamaA.19900.a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5746
Polymers43,2121
Non-polymers3625
Water1,20767
1
A: BamaA.19900.a
hetero molecules

A: BamaA.19900.a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,14912
Polymers86,4242
Non-polymers72510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation19_444-x-1/4,-z-1/4,-y-1/41
Buried area5580 Å2
ΔGint-35 kcal/mol
Surface area28680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.300, 157.300, 157.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Space group name HallP4bd2ab3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4
Components on special symmetry positions
IDModelComponents
11A-403-

CA

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Components

#1: Protein BamaA.19900.a


Mass: 43212.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Balamuthia mandrillaris (eukaryote) / Strain: CDC:V039: baboon/San Diego/1986 / Plasmid: BamaA.19900.a.MP3 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
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: 3.75 Å3/Da / Density % sol: 67.23 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 8.35 mg/mL BamaA.19900.a.MP3.PS38592 in 2 mM glucose, 2 mM AMPPNP, 2 mM magnesium chloride against RigakuReagents Wizard 3/4 screen, condition E11 (30% v/v PEG300, 200 mM calcium acetate, ...Details: 8.35 mg/mL BamaA.19900.a.MP3.PS38592 in 2 mM glucose, 2 mM AMPPNP, 2 mM magnesium chloride against RigakuReagents Wizard 3/4 screen, condition E11 (30% v/v PEG300, 200 mM calcium acetate, 100 mM sodium cacodylate/HCl, pH 6.5), direct cryoprotection, tray 311701e11, puck zcg0-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 20, 2020
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 19871 / % possible obs: 99.6 % / Redundancy: 13.219 % / Biso Wilson estimate: 50.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.095 / Χ2: 1.024 / Net I/σ(I): 22.86
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.7213.50.6055.1614310.9430.628100
2.72-2.7913.5770.4856.3314010.9660.503100
2.79-2.8713.5470.4067.5713550.9730.422100
2.87-2.9613.5010.3159.5513460.9810.327100
2.96-3.0613.4960.25111.4512800.9910.261100
3.06-3.1713.4690.18914.6512450.9930.197100
3.17-3.2913.3950.16416.7812220.9930.171100
3.29-3.4213.3710.12920.0611710.9960.134100
3.42-3.5713.3360.10323.7911120.9980.107100
3.57-3.7513.2470.08229.0110840.9980.086100
3.75-3.9513.2680.07133.3610230.9980.07499.8
3.95-4.1913.1690.06535.399700.9980.06899.8
4.19-4.4813.0910.05838.429200.9980.06199.8
4.48-4.8413.0010.05440.598670.9980.05699.5
4.84-5.312.9880.05439.248010.9980.05799.3
5.3-5.9312.860.05637.837220.9980.05999.2
5.93-6.8412.7070.05339.36480.9980.05598.2
6.84-8.3812.5310.04643.685540.9980.04997.5
8.38-11.8511.9280.03946.834460.9990.04197.4
11.85-509.8720.04143.32730.9970.04391.9

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Processing

Software
NameVersionClassification
PHENIX1.18refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
MoRDaphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3 domains of PDB entry 6DA0 as per MORDA

6da0


Resolution: 2.65→49.74 Å / SU ML: 0.2467 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.0432
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 2052 10.34 %0
Rwork0.1743 17799 --
obs0.1774 19851 99.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.41 Å2
Refinement stepCycle: LAST / Resolution: 2.65→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2824 0 19 67 2910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00542896
X-RAY DIFFRACTIONf_angle_d0.75513939
X-RAY DIFFRACTIONf_chiral_restr0.0446457
X-RAY DIFFRACTIONf_plane_restr0.0048511
X-RAY DIFFRACTIONf_dihedral_angle_d20.15871017
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.710.2491510.22281156X-RAY DIFFRACTION100
2.71-2.780.23471280.19441147X-RAY DIFFRACTION100
2.78-2.850.22031340.1931160X-RAY DIFFRACTION99.92
2.86-2.940.25221160.20881173X-RAY DIFFRACTION100
2.94-3.030.25651360.21631188X-RAY DIFFRACTION100
3.03-3.140.24911300.20521149X-RAY DIFFRACTION100
3.14-3.270.24031300.2121177X-RAY DIFFRACTION100
3.27-3.420.2741350.19531191X-RAY DIFFRACTION100
3.42-3.60.21510.191158X-RAY DIFFRACTION100
3.6-3.820.18521380.16531165X-RAY DIFFRACTION100
3.82-4.120.1981360.14721202X-RAY DIFFRACTION99.93
4.12-4.530.15171410.13991193X-RAY DIFFRACTION99.85
4.53-5.180.18531270.14471219X-RAY DIFFRACTION99.78
5.19-6.530.21381490.17071224X-RAY DIFFRACTION99.42
6.53-49.740.17271500.17381297X-RAY DIFFRACTION97.44
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)
15.02805126462-1.50838013754.151666330432.6606424048-2.326298303295.902923822930.07053629698940.08465224174840.05732045314880.2470818301450.00658469381998-0.231966300996-0.2827653021830.0713076350555-0.05321807996730.4630654343010.08970662200670.03979200110560.2377835934-0.009720331594150.3820172804149.35313216018-54.293686500715.78234387
24.78377759113-3.07217037897-1.036437129014.959779111381.527756796621.166664192190.0728090581901-0.1541602221760.07533321925640.3516311237410.0779135312534-0.1523794640540.1706506447310.0406079152739-0.137232177470.4097888961330.04065116354620.01794508710320.2805570613670.05547536984920.248150703414-6.70120887776-47.961686303216.6273360269
32.44986687783-0.2061350558460.6471897109951.032511845570.3397027886972.014613048350.03495662291830.1270768021160.583727858223-0.2331797020580.0288066467012-0.212463996676-0.2993866588480.262126330892-0.01279653376270.4768630553780.05095093593670.155716445410.2957845322550.08965606581170.451550913965-9.04679777961-31.87608157985.15507657802
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 109 )2 - 1091 - 108
22chain 'A' and (resid 110 through 201 )110 - 201109 - 195
33chain 'A' and (resid 202 through 380 )202 - 380196 - 374

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