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- PDB-3mcp: Crystal structure of Glucokinase (BDI_1628) from Parabacteroides ... -

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Basic information

Entry
Database: PDB / ID: 3mcp
TitleCrystal structure of Glucokinase (BDI_1628) from Parabacteroides distasonis ATCC 8503 at 3.00 A resolution
ComponentsGlucokinase
KeywordsTRANSFERASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


ROK family / ROK family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Glucokinase
Similarity search - Component
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Glucokinase (BDI_1628) from Parabacteroides distasonis ATCC 8503 at 3.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5294
Polymers39,2981
Non-polymers2303
Water23413
1
A: Glucokinase
hetero molecules

A: Glucokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,0578
Polymers78,5972
Non-polymers4606
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area6220 Å2
ΔGint-39 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.732, 80.732, 142.581
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Glucokinase


Mass: 39298.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_1628 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LCG6
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DNA SEQUENCING OF THE CLONED CONSTRUCT REVEALS A GLYCINE AT POSITION 61 INSTEAD OF AN ASPARTATE AND A GLUTAMATE AT POSITION 306 INSTEAD OF AN ASPARTATE. THE GLYCINE AT POSITION 61 AND GLUTAMATE AT POSITION 306 ARE SUPPORTED BY THE ELECTRON DENSITY.

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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: 2.96 Å3/Da / Density % sol: 58.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 10.0000% Glycerol, 3.6000M NaFormate, No Buffer pH 7.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97911
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 30, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979111
ReflectionResolution: 3→28.748 Å / Num. obs: 10015 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 70.492 Å2 / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 14.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3-3.087.30.7161.152327140.716100
3.08-3.167.20.6051.350226970.605100
3.16-3.257.20.4781.649686910.478100
3.25-3.357.20.375247906630.375100
3.35-3.467.20.3222.345876410.322100
3.46-3.597.20.2393.245006280.239100
3.59-3.727.20.193.943606070.19100
3.72-3.877.10.1644.641395810.164100
3.87-4.057.10.1415.240235670.141100
4.05-4.247.10.1156.538905460.115100
4.24-4.4770.16.935765100.1100
4.47-4.7470.097.934754950.09100
4.74-5.076.90.089.131774580.08100
5.07-5.486.90.0878.330664420.087100
5.48-66.90.091827704040.091100
6-6.716.80.0838.725863800.083100
6.71-7.756.60.05811.721583260.058100
7.75-9.496.40.04713.618862930.047100
9.49-13.426.10.0415.214452380.04100
13.42-28.755.20.046137031340.04690.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3→28.748 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.907 / Occupancy max: 1 / Occupancy min: 0.75 / SU B: 18.642 / SU ML: 0.336 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.4
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.2.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. GLYCEROL (GOL) AND FORMIC ACID FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 477 4.8 %RANDOM
Rwork0.206 ---
obs0.209 9970 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 94.43 Å2 / Biso mean: 53.803 Å2 / Biso min: 22.42 Å2
Baniso -1Baniso -2Baniso -3
1--1.8 Å20 Å20 Å2
2---1.8 Å20 Å2
3---3.6 Å2
Refinement stepCycle: LAST / Resolution: 3→28.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2590 0 15 13 2618
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222650
X-RAY DIFFRACTIONr_bond_other_d0.0010.021770
X-RAY DIFFRACTIONr_angle_refined_deg0.9191.983584
X-RAY DIFFRACTIONr_angle_other_deg0.68234318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3965353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.81224.369103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33515406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.1171514
X-RAY DIFFRACTIONr_chiral_restr0.060.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213023
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02533
X-RAY DIFFRACTIONr_mcbond_it0.83921746
X-RAY DIFFRACTIONr_mcbond_other0.0642739
X-RAY DIFFRACTIONr_mcangle_it1.72242757
X-RAY DIFFRACTIONr_scbond_it2.5786904
X-RAY DIFFRACTIONr_scangle_it4.4378827
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 30 -
Rwork0.297 680 -
all-710 -
obs--99.72 %

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