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- PDB-3fhl: Crystal structure of a putative oxidoreductase from bacteroides f... -

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Basic information

Entry
Database: PDB / ID: 3fhl
TitleCrystal structure of a putative oxidoreductase from bacteroides fragilis nctc 9343
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / NAD-BINDING DOMAIN / PSI-2 / NYSGXRC / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich ...Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative oxidoreductase
Similarity search - Component
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
AuthorsPatskovsky, Y. / Ramagopal, U. / Toro, R. / Gilmore, M. / Miller, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of a Putative Oxidoreductase from Bacteroides Fragilis Nctc 9343
Authors: Patskovsky, Y. / Ramagopal, U. / Toro, R. / Gilmore, M. / Miller, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionDec 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative oxidoreductase
B: Putative oxidoreductase
C: Putative oxidoreductase
D: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,3038
Polymers164,0704
Non-polymers2334
Water18,3571019
1
A: Putative oxidoreductase
C: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2445
Polymers82,0352
Non-polymers2083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-16 kcal/mol
Surface area28750 Å2
MethodPISA
2
B: Putative oxidoreductase
D: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0593
Polymers82,0352
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-5 kcal/mol
Surface area28790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.258, 127.367, 79.889
Angle α, β, γ (deg.)90.00, 112.01, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 6 / Auth seq-ID: 2 - 351 / Label seq-ID: 4 - 353

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12CC
22DD

NCS ensembles :
ID
1
2

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Components

#1: Protein
Putative oxidoreductase /


Mass: 41017.559 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Gene: BF2340 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5LCX7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1019 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M SODIUM CACODYLATE, PH 6.5, 20% PEG8000, 0.2M MAGNESIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 6, 2008 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 138748 / % possible obs: 99.4 % / Observed criterion σ(I): -5 / Redundancy: 3.3 % / Biso Wilson estimate: 32.18 Å2 / Rsym value: 0.075 / Net I/σ(I): 6.7
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.1 / % possible all: 95.2

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.2.0019refinement
DENZOdata reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.93→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.545 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21503 4098 3 %RANDOM
Rwork0.18601 ---
obs0.1869 131517 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.578 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å22.99 Å2
2--0.69 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.93→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10537 0 14 1019 11570
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02211030
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.96614968
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28451393
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91824.114525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.794151972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4781566
X-RAY DIFFRACTIONr_chiral_restr0.0820.21645
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028370
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1550.34982
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.57411
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.51655
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0610.54
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.374
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.542
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.27726899
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.246310767
X-RAY DIFFRACTIONr_scbond_it5.02534697
X-RAY DIFFRACTIONr_scangle_it6.7554158
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2456loose positional0.460.5
2C2648loose positional0.360.5
1A2456loose thermal6.455
2C2648loose thermal4.555
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 277 -
Rwork0.271 9601 -
obs--98.78 %

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