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- PDB-3ijr: 2.05 Angstrom resolution crystal structure of a short chain dehyd... -

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Basic information

Entry
Database: PDB / ID: 3ijr
Title2.05 Angstrom resolution crystal structure of a short chain dehydrogenase from Bacillus anthracis str. 'Ames Ancestor' in complex with NAD+
ComponentsOxidoreductase, short chain dehydrogenase/reductase family
KeywordsOXIDOREDUCTASE / Short Chain Dehydrogenase / Structural Genomics / Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


oxidoreductase activity, acting on CH-OH group of donors / nucleotide binding / metal ion binding
Similarity search - Function
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Oxidoreductase, short chain dehydrogenase/reductase family / Oxidoreductase, short chain dehydrogenase/reductase family
Similarity search - Component
Biological speciesBacillus anthracis str. 'Ames Ancestor' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHalavaty, A.S. / Minasov, G. / Skarina, T. / Onopriyenko, O. / Gordon, E. / Kwon, K. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 2.05 Angstrom resolution crystal structure of a short chain dehydrogenase from Bacillus anthracis str. 'Ames Ancestor' in complex with NAD+
Authors: Halavaty, A.S. / Minasov, G. / Skarina, T. / Onopriyenko, O. / Gordon, E. / Kwon, K. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase, short chain dehydrogenase/reductase family
B: Oxidoreductase, short chain dehydrogenase/reductase family
C: Oxidoreductase, short chain dehydrogenase/reductase family
D: Oxidoreductase, short chain dehydrogenase/reductase family
E: Oxidoreductase, short chain dehydrogenase/reductase family
F: Oxidoreductase, short chain dehydrogenase/reductase family
G: Oxidoreductase, short chain dehydrogenase/reductase family
H: Oxidoreductase, short chain dehydrogenase/reductase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,13638
Polymers255,2898
Non-polymers6,84730
Water16,790932
1
A: Oxidoreductase, short chain dehydrogenase/reductase family
B: Oxidoreductase, short chain dehydrogenase/reductase family
C: Oxidoreductase, short chain dehydrogenase/reductase family
D: Oxidoreductase, short chain dehydrogenase/reductase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,16420
Polymers127,6454
Non-polymers3,51916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14530 Å2
ΔGint-80.6 kcal/mol
Surface area35030 Å2
MethodPISA
2
E: Oxidoreductase, short chain dehydrogenase/reductase family
F: Oxidoreductase, short chain dehydrogenase/reductase family
G: Oxidoreductase, short chain dehydrogenase/reductase family
H: Oxidoreductase, short chain dehydrogenase/reductase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,97218
Polymers127,6454
Non-polymers3,32714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14970 Å2
ΔGint-87.2 kcal/mol
Surface area36070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.749, 123.203, 169.767
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11E-331-

HOH

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Components

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


Mass: 31911.139 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. 'Ames Ancestor' (bacteria)
Strain: Ames Ancestor / Gene: BAS0712, BA_0748, GBAA0748, GBAA_0748 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3) / References: UniProt: Q81UV8, UniProt: A0A6L8PL20*PLUS
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 932 / 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: 2.31 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350, 0.2M Ammonium sulfate, 0.1M Bis-Tris pH 5.5, 10mm NAD+. Paratone-N used as a cryoprotectant , VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 7, 2009 / Details: Beryllium Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 284777 / Num. obs: 284777 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 17.19
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.99 / Num. unique all: 14257 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3I3O

3i3o


Resolution: 2.05→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 8.861 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. The Friedel pairs were used in phasing. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3. Authors used TLS in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.19348 7373 5 %RANDOM
Rwork0.15709 ---
all0.15891 139930 --
obs0.15891 139930 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.358 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å2-0 Å2-0 Å2
2--0.71 Å20 Å2
3----2.14 Å2
Refinement stepCycle: LAST / Resolution: 2.05→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17344 0 430 932 18706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02218481
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212101
X-RAY DIFFRACTIONr_angle_refined_deg1.421.9925207
X-RAY DIFFRACTIONr_angle_other_deg0.818329923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.19952334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3126.233815
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.923153071
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3551548
X-RAY DIFFRACTIONr_chiral_restr0.0820.22801
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02120681
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023243
X-RAY DIFFRACTIONr_mcbond_it0.9661.511484
X-RAY DIFFRACTIONr_mcbond_other0.3321.54680
X-RAY DIFFRACTIONr_mcangle_it1.54218603
X-RAY DIFFRACTIONr_scbond_it2.83836997
X-RAY DIFFRACTIONr_scangle_it4.1464.56604
LS refinement shellResolution: 2.05→2.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 494 -
Rwork0.176 9811 -
obs-9811 95.3 %
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)
12.5855-0.22961.62322.3309-0.462.34270.17840.2331-0.2814-0.1007-0.1049-0.60360.25410.4549-0.07360.1858-0.14390.04530.38040.00320.53660.715939.0319-72.1767
21.42690.7951-0.03671.2522-0.31471.180.1536-0.12830.01150.1844-0.1327-0.2079-0.10220.2069-0.02090.1905-0.2191-0.0280.2704-0.01560.3543-5.983848.791-61.647
31.69331.3222-0.13481.6429-0.22122.19250.1464-0.09450.13530.0522-0.11310.0286-0.0052-0.0383-0.03330.1683-0.18930.01360.2435-0.02920.2818-19.058242.8914-62.7327
43.69352.31211.76652.81312.39813.15370.2745-0.3214-0.54490.3403-0.1627-0.67010.38230.1686-0.11180.2847-0.1218-0.07830.37840.05830.6145-0.983727.4958-63.7186
52.16940.7952-0.0922.2614-0.19041.1844-0.02990.1222-0.1097-0.04510.0612-0.23280.090.064-0.03130.1351-0.1570.0090.2123-0.02050.2518-15.071736.5661-73.4873
63.70260.27840.26592.57680.65891.5447-0.27240.32330.6085-0.36190.19160.5202-0.2752-0.36880.08080.337-0.1414-0.06530.38690.16450.3784-33.256644.361-89.3682
72.40660.8394-0.20612.7780.40641.8309-0.38620.59230.2171-0.63950.33950.1963-0.2221-0.22920.04670.3395-0.2908-0.03730.41080.06410.1356-26.778135.488-94.9008
81.53930.972-0.27321.426-0.18961.742-0.19640.3724-0.0283-0.34590.2487-0.01020.1289-0.1598-0.05230.2507-0.24090.00180.3083-0.00810.2027-29.915326.0215-87.1098
96.56184.82243.34063.54622.46492.1832-0.1511-0.25221.0275-0.1438-0.18320.76380.0886-0.73840.33430.385-0.1866-0.13330.79030.16090.7335-43.182442.2192-80.8105
101.64490.8096-0.54722.45490.20241.278-0.05740.17580.1752-0.10290.07050.1035-0.0845-0.1202-0.0130.1285-0.1469-0.00850.20680.01870.1932-24.215838.9743-77.8765
115.1029-3.56451.68816.1564-0.93480.77760.4271-0.0421-1.03890.18460.0074-0.40370.36940.2702-0.43450.7618-0.0835-0.16260.6452-0.02310.7297-30.042-1.908-60.5726
121.33650.6184-0.31351.6176-0.08270.96290.1119-0.0875-0.21670.08-0.0342-0.09520.3016-0.1541-0.07760.3198-0.3025-0.03220.3213-0.00260.2847-44.76675.9653-63.2107
132.17091.1064-0.32921.8969-0.02551.7123-0.00810.0576-0.0163-0.03050.03230.01450.1936-0.1585-0.02420.2111-0.2285-0.0170.25230.00270.2247-39.591218.206-69.265
142.05660.5448-0.04682.2166-0.16380.95160.16740.0389-0.5597-0.0607-0.1219-0.6790.37260.1541-0.04550.3816-0.1853-0.04420.32450.00910.513-25.51786.4351-60.748
152.77980.2383-0.42021.932-0.21880.53710.1886-0.076-0.07830.1563-0.1525-0.02230.0597-0.0998-0.03610.2114-0.2356-0.01420.2731-0.01150.1864-34.363922.6382-56.4783
162.42820.27350.35674.69830.56490.88340.2899-0.32360.3610.4836-0.25190.5191-0.0918-0.3229-0.0380.4001-0.26080.16150.5101-0.12380.3336-43.273538.3754-38.8397
171.80340.7169-0.17731.6306-0.42921.53580.3638-0.6156-0.01030.559-0.3617-0.05940.0084-0.0184-0.00220.4594-0.4308-0.03090.5123-0.010.1446-29.449928.037-32.4896
181.46410.962-0.15512.0328-0.23131.48440.3169-0.3570.06410.3964-0.3054-0.0884-0.0499-0.0153-0.01150.2589-0.2824-0.01130.3278-0.02270.2063-23.265335.1411-47.512
191.61240.7618-0.13030.44210.22811.36160.2531-0.19650.51980.1132-0.20310.2934-0.3157-0.2569-0.050.3572-0.19670.11370.3916-0.09890.4119-41.57238.8248-48.462
202.12140.6987-0.01872.1566-0.26980.27650.2021-0.1979-0.09210.3047-0.2423-0.05010.0383-0.04070.04020.2332-0.2474-0.00640.27-0.0130.1583-31.382122.7598-53.5007
212.6550.98882.0741.97870.99724.17150.0334-0.3003-0.2020.1252-0.15240.6804-0.0516-1.23150.11910.56380.2960.14120.8696-0.04040.7867-106.088349.0758-13.001
221.3563-0.6285-0.18792.39031.12173.140.05270.04740.1009-0.1327-0.14110.533-0.7789-0.72050.08840.47780.45040.00350.42640.01520.4139-98.614957.6103-22.1543
230.7129-1.148-0.27992.93241.36133.48860.06030.05750.162-0.0411-0.05130.1764-0.5002-0.28-0.00890.34380.27810.05450.25530.0320.2623-86.425850.4456-23.4468
241.78242.4602-1.94445.5282-2.37662.2396-0.11780.584-0.0340.1908-0.15551.22960.392-1.00050.27320.7248-0.0320.27851.6038-0.40671.2481-104.756138.3738-17.9449
251.49190.2484-0.04472.11630.50262.722-0.0876-0.08450.14130.2090.06440.262-0.1727-0.29120.02320.32430.27620.06350.26160.0250.226-86.103545.1243-11.5512
261.6211-0.09-0.33012.10310.25771.7502-0.0982-0.15340.36010.28250.1972-0.3943-0.27070.4065-0.0990.59690.1894-0.02340.45-0.0820.3409-70.70547.14021.2639
271.1156-0.6402-0.82461.43520.99592.097-0.221-0.29470.01560.68260.21850.01520.14230.19910.00250.66280.34860.05540.38670.01270.153-78.071236.318410.7812
280.9282-1.0023-0.46412.19260.6142.5689-0.2901-0.2057-0.0970.56410.25070.10150.31990.05620.03940.43350.27510.06970.24940.03010.143-77.428228.8976-3.6878
291.8949-3.07882.17615.523-3.47947.3208-0.2263-0.18170.48980.58730.2083-0.7988-0.03970.85870.0180.53960.2009-0.10660.5419-0.15010.4811-62.458144.7789-4.1932
300.7695-0.4512-0.48882.12180.73522.9637-0.1239-0.15960.15880.33890.14360.0083-0.1158-0.0077-0.01970.38150.25160.05840.25290.00720.176-81.5844.2602-6.7931
312.49191.2111-1.65342.7416-0.9613.0738-0.30740.1981-0.44440.14130.19950.57310.81-0.48110.10790.73560.04350.11280.3460.0370.6042-81.90713.5336-25.0255
320.8919-0.3417-0.4141.64510.59191.7326-0.1674-0.0927-0.1480.36270.18810.06150.61450.1909-0.02070.52980.30950.05810.2410.04920.2075-67.18339.0569-19.3974
330.7917-1.4094-0.59392.5171.06113.2797-0.2419-0.18170.01860.37910.2832-0.03990.48420.291-0.04130.39120.29970.02510.23210.02350.1458-69.182722.2859-18.1673
342.6736-4.03692.25518.487-3.74185.5268-0.381-0.3215-0.38050.68090.33571.04410.7484-0.96510.04530.6857-0.00540.21650.51540.04130.6676-89.754811.082-20.3221
351.9128-0.4598-0.24272.0380.78511.9294-0.0477-0.0576-0.180.08730.03870.09660.2643-0.04420.0090.27360.18590.02660.19250.03370.1533-75.126521.9875-29.3351
361.61580.3357-0.22453.2265-0.06361.51980.19750.08730.1529-0.4477-0.0306-0.6003-0.34750.4552-0.16690.48560.06490.16580.40910.0010.3437-62.797435.7987-45.5947
371.03-0.7346-0.3122.52570.81522.34610.2590.23880.0784-0.7167-0.18280.0135-0.3721-0.1212-0.07610.45540.22890.01250.27110.06010.1463-78.367137.8335-49.9409
380.7106-1.2374-0.51193.0560.63962.80060.1090.0913-0.0319-0.4217-0.10090.3173-0.3306-0.3804-0.00810.29840.2286-0.01980.26840.03430.1737-83.638837.3074-37.539
391.0032-0.44411.40892.0010.47412.8069-0.18780.10080.2762-0.21970.342-0.9036-0.71360.4594-0.15420.6406-0.0050.24380.4781-0.05670.5727-62.900243.3776-35.7679
401.5168-0.2337-0.15222.00670.72921.7933-0.02340.0257-0.0313-0.06310.03290.11360.1239-0.0725-0.00940.24820.17950.01950.2050.04020.1347-76.107527.2811-32.7459
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 43
2X-RAY DIFFRACTION2A44 - 164
3X-RAY DIFFRACTION3A165 - 225
4X-RAY DIFFRACTION4A226 - 249
5X-RAY DIFFRACTION5A250 - 288
6X-RAY DIFFRACTION6B6 - 44
7X-RAY DIFFRACTION7B45 - 82
8X-RAY DIFFRACTION8B83 - 225
9X-RAY DIFFRACTION9B226 - 248
10X-RAY DIFFRACTION10B249 - 288
11X-RAY DIFFRACTION11C8 - 36
12X-RAY DIFFRACTION12C37 - 144
13X-RAY DIFFRACTION13C145 - 226
14X-RAY DIFFRACTION14C227 - 264
15X-RAY DIFFRACTION15C265 - 288
16X-RAY DIFFRACTION16D8 - 37
17X-RAY DIFFRACTION17D38 - 133
18X-RAY DIFFRACTION18D134 - 229
19X-RAY DIFFRACTION19D230 - 263
20X-RAY DIFFRACTION20D264 - 288
21X-RAY DIFFRACTION21E9 - 43
22X-RAY DIFFRACTION22E44 - 152
23X-RAY DIFFRACTION23E153 - 225
24X-RAY DIFFRACTION24E226 - 259
25X-RAY DIFFRACTION25E260 - 288
26X-RAY DIFFRACTION26F-1 - 46
27X-RAY DIFFRACTION27F47 - 138
28X-RAY DIFFRACTION28F139 - 225
29X-RAY DIFFRACTION29F226 - 249
30X-RAY DIFFRACTION30F250 - 288
31X-RAY DIFFRACTION31G8 - 37
32X-RAY DIFFRACTION32G38 - 157
33X-RAY DIFFRACTION33G158 - 227
34X-RAY DIFFRACTION34G228 - 251
35X-RAY DIFFRACTION35G252 - 288
36X-RAY DIFFRACTION36H0 - 44
37X-RAY DIFFRACTION37H45 - 148
38X-RAY DIFFRACTION38H149 - 229
39X-RAY DIFFRACTION39H230 - 258
40X-RAY DIFFRACTION40H259 - 288

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