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- PDB-3t4x: Short chain dehydrogenase/reductase family oxidoreductase from Ba... -

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Basic information

Entry
Database: PDB / ID: 3t4x
TitleShort chain dehydrogenase/reductase family oxidoreductase from Bacillus anthracis str. Ames Ancestor
ComponentsOxidoreductase, short chain dehydrogenase/reductase family
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


: / short chain dehydrogenase / 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
Oxidoreductase, short chain dehydrogenase/reductase family / Oxidoreductase, short chain dehydrogenase/reductase family
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Skarina, T. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Short chain dehydrogenase/reductase family oxidoreductase from Bacillus anthracis str. 'Ames Ancestor'
Authors: Filippova, E.V. / Wawrzak, Z. / Skarina, T. / Edwards, A. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxidoreductase, short chain dehydrogenase/reductase family
B: Oxidoreductase, short chain dehydrogenase/reductase family


Theoretical massNumber of molelcules
Total (without water)59,9822
Polymers59,9822
Non-polymers00
Water36020
1
A: Oxidoreductase, short chain dehydrogenase/reductase family
B: Oxidoreductase, short chain dehydrogenase/reductase family

A: Oxidoreductase, short chain dehydrogenase/reductase family
B: Oxidoreductase, short chain dehydrogenase/reductase family


Theoretical massNumber of molelcules
Total (without water)119,9634
Polymers119,9634
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area15570 Å2
ΔGint-106 kcal/mol
Surface area38890 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-25 kcal/mol
Surface area24170 Å2
MethodPISA
3
A: Oxidoreductase, short chain dehydrogenase/reductase family

A: Oxidoreductase, short chain dehydrogenase/reductase family


Theoretical massNumber of molelcules
Total (without water)59,9822
Polymers59,9822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3850 Å2
ΔGint-24 kcal/mol
Surface area23320 Å2
MethodPISA
4
B: Oxidoreductase, short chain dehydrogenase/reductase family

B: Oxidoreductase, short chain dehydrogenase/reductase family


Theoretical massNumber of molelcules
Total (without water)59,9822
Polymers59,9822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3810 Å2
ΔGint-27 kcal/mol
Surface area23480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.979, 144.979, 65.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 4 / Auth seq-ID: 1 - 264 / Label seq-ID: 4 - 267

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Oxidoreductase, short chain dehydrogenase/reductase family


Mass: 29990.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS3188, BA_3440, GBAA_3440 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q81MX9, UniProt: A0A384KDK1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Tacsimate 60%,NaCl 0.2M, CaAcetate 5mM, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.06885 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2011 / Details: MIRRORS
RadiationMonochromator: SE {111} CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06885 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 17682 / Num. obs: 17682 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 89.9 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 19.04
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1572 / % possible all: 89.8

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.935 / SU B: 34.481 / SU ML: 0.305 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.943 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26278 895 5.1 %RANDOM
Rwork0.20017 ---
obs0.20331 16691 98 %-
all-16691 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.352 Å2
Baniso -1Baniso -2Baniso -3
1--3.97 Å20 Å20 Å2
2---3.97 Å20 Å2
3---7.94 Å2
Refine analyzeLuzzati coordinate error obs: 0.5 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4062 0 0 20 4082
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224116
X-RAY DIFFRACTIONr_angle_refined_deg1.9521.9785568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.2985528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.59125168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17415760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9751525
X-RAY DIFFRACTIONr_chiral_restr0.1350.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213007
X-RAY DIFFRACTIONr_mcbond_it0.9461.52636
X-RAY DIFFRACTIONr_mcangle_it1.73324280
X-RAY DIFFRACTIONr_scbond_it3.54831480
X-RAY DIFFRACTIONr_scangle_it5.494.51288
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2017 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.510.5
Bmedium thermal1.182
LS refinement shellResolution: 2.8→2.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 58 -
Rwork0.252 1090 -
obs--88.38 %
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)
13.4134-0.6735-0.28032.39570.90231.6869-0.0976-0.78440.56530.45520.1775-0.034-0.18990.1473-0.07990.2494-0.0455-0.00890.2268-0.1130.108132.250943.867512.8062
24.3038-0.53090.04563.41270.6271.7874-0.0759-0.177-0.56690.2476-0.13521.3540.0727-0.58330.21110.0886-0.05480.12170.2308-0.02570.5885.585425.74655.1722
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 264
2X-RAY DIFFRACTION2B0 - 264

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