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- PDB-4mow: Crystal structure of a putative glucose 1-dehydrogenase from Burk... -

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Basic information

Entry
Database: PDB / ID: 4mow
TitleCrystal structure of a putative glucose 1-dehydrogenase from Burkholderia cenocepacia J2315
ComponentsGlucose 1-dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / dehydrogenase
Function / homology
Function and homology information


glucose 1-dehydrogenase [NAD(P)+] activity / glucose 1-dehydrogenase [NAD(P)+] / nucleotide binding / metal ion binding
Similarity search - Function
PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glucose 1-dehydrogenase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a putative glucose 1-dehydrogenase from Burkholderia cenocepacia J2315
Authors: Lukacs, C.M. / Fairman, J.W. / Edwards, T.E. / Lorimer, D.
History
DepositionSep 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 22, 2025Group: Structure summary / Category: audit_author / pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose 1-dehydrogenase
B: Glucose 1-dehydrogenase
C: Glucose 1-dehydrogenase
D: Glucose 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,70612
Polymers104,5224
Non-polymers1848
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-80 kcal/mol
Surface area31990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.990, 82.380, 168.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glucose 1-dehydrogenase


Mass: 26130.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / LMG 16656 / Gene: BCAL1425, BceJ2315_13920, J2315 / Production host: Escherichia coli (E. coli)
References: UniProt: B4E6Z1, glucose 1-dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 46.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus G4: 37.5% MPD_P1K_P3350, 0.1M carboxylic acids, 0.1M buffer 1 pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 70830 / Num. obs: 70165 / % possible obs: 99.1 % / Redundancy: 6.32 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.35
Reflection shellResolution: 1.95→2 Å / Redundancy: 6.38 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 4.03 / Num. unique all: 5164 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JIG

4jig


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.708 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19848 3542 5.1 %RANDOM
Rwork0.15865 ---
obs0.16069 66568 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.232 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---0.54 Å2-0 Å2
3---1 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6820 0 8 522 7350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196898
X-RAY DIFFRACTIONr_bond_other_d0.0010.026719
X-RAY DIFFRACTIONr_angle_refined_deg1.5431.9599412
X-RAY DIFFRACTIONr_angle_other_deg0.835315340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8355962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.57424.706238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.285151012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9631536
X-RAY DIFFRACTIONr_chiral_restr0.0960.21176
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028056
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021428
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_it1.5251.9513872
X-RAY DIFFRACTIONr_mcbond_other1.5251.9513871
X-RAY DIFFRACTIONr_mcangle_it2.2442.9134826
X-RAY DIFFRACTIONr_mcangle_other2.2432.9124827
X-RAY DIFFRACTIONr_scbond_it2.072.1373026
X-RAY DIFFRACTIONr_scbond_other2.072.1373026
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2143.1134586
X-RAY DIFFRACTIONr_long_range_B_refined5.4716.5338161
X-RAY DIFFRACTIONr_long_range_B_other5.34716.1497914
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 253 -
Rwork0.192 4854 -
obs--99.88 %
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)
10.08980.06090.13230.48690.10130.3023-0.01190.0352-0.01580.08350.0472-0.1605-0.0215-0.0114-0.03530.02270.0046-0.02880.053-0.00990.0566-3.5708-23.462627.2277
20.1505-0.05750.1260.60520.08620.1429-0.0643-0.03250.03260.03630.0050.0964-0.0587-0.04410.05940.04240.0389-0.0040.0588-0.00060.0504-31.4321-14.162523.5977
30.06740.06890.07940.8059-0.09430.13630.06-0.0021-0.0720.03570.0267-0.09840.0862-0.0147-0.08670.07490.0038-0.07220.0157-0.00080.0784-13.4652-53.206223.6214
40.2633-0.2030.11850.67270.13470.1620.08480.0359-0.0866-0.0927-0.10250.2140.035-0.04730.01770.0398-0.0179-0.04740.1069-0.0020.0825-38.3072-41.850511.2372
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 248
2X-RAY DIFFRACTION2B1 - 248
3X-RAY DIFFRACTION3C2 - 248
4X-RAY DIFFRACTION4D2 - 248

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