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- PDB-4iuy: Crystal structure of short-chain dehydrogenase/reductase (apo-for... -

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Basic information

Entry
Database: PDB / ID: 4iuy
TitleCrystal structure of short-chain dehydrogenase/reductase (apo-form) from A. baumannii clinical strain WM99C
ComponentsShort chain dehydrogenase/reductase
KeywordsOXIDOREDUCTASE / Rossmann Fold
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
Dehydrogenase with different specificities
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.385 Å
AuthorsShah, B.S. / Tetu, S.G. / Harrop, S.J. / Paulsen, I.T. / Mabbutt, B.C.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Structure of a short-chain dehydrogenase/reductase (SDR) within a genomic island from a clinical strain of Acinetobacter baumannii.
Authors: Shah, B.S. / Tetu, S.G. / Harrop, S.J. / Paulsen, I.T. / Mabbutt, B.C.
History
DepositionJan 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Advisory / Database references / Derived calculations
Category: citation / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Short chain dehydrogenase/reductase
B: Short chain dehydrogenase/reductase
E: Short chain dehydrogenase/reductase
C: Short chain dehydrogenase/reductase
H: Short chain dehydrogenase/reductase
D: Short chain dehydrogenase/reductase
F: Short chain dehydrogenase/reductase
G: Short chain dehydrogenase/reductase


Theoretical massNumber of molelcules
Total (without water)242,7898
Polymers242,7898
Non-polymers00
Water9,566531
1
A: Short chain dehydrogenase/reductase
B: Short chain dehydrogenase/reductase
C: Short chain dehydrogenase/reductase
D: Short chain dehydrogenase/reductase


Theoretical massNumber of molelcules
Total (without water)121,3944
Polymers121,3944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12490 Å2
ΔGint-95 kcal/mol
Surface area37760 Å2
MethodPISA
2
E: Short chain dehydrogenase/reductase
H: Short chain dehydrogenase/reductase
F: Short chain dehydrogenase/reductase
G: Short chain dehydrogenase/reductase


Theoretical massNumber of molelcules
Total (without water)121,3944
Polymers121,3944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12320 Å2
ΔGint-91 kcal/mol
Surface area38130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.219, 89.525, 120.905
Angle α, β, γ (deg.)90.00, 112.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Short chain dehydrogenase/reductase / Dehydrogenase with different specificities


Mass: 30348.564 Da / Num. of mol.: 8 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Strain: WM99C, ACICU / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: A0A7U3Y0F0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE CORRESPONDS TO GENBANK ENTRY EMD81570.1.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.1843.69
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop7.50.14 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 18.65% v/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting drop7.50.16 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 20% v/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAustralian Synchrotron MX110.9537
SYNCHROTRONAustralian Synchrotron MX120.9794
Detector
TypeIDDetectorDate
ADSC QUANTUM 210r1CCDJul 5, 2012
ADSC QUANTUM 210r2CCDJul 5, 2012
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
20.97941
ReflectionResolution: 2.385→19.76 Å / Num. all: 81772 / Num. obs: 81772 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 15.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CCP4model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4G81

4g81


Resolution: 2.385→19.76 Å / SU ML: 0.3 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 0 / Phase error: 22.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 1993 2.44 %RANDOM
Rwork0.1546 ---
obs0.1558 81728 98.11 %-
all-81728 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.385→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15617 0 0 531 16148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815905
X-RAY DIFFRACTIONf_angle_d1.15621541
X-RAY DIFFRACTIONf_dihedral_angle_d12.7495868
X-RAY DIFFRACTIONf_chiral_restr0.0742514
X-RAY DIFFRACTIONf_plane_restr0.0052794
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.385-2.4450.3959910.28124265435674
2.445-2.5110.2981360.230858245960100
2.511-2.58470.2841420.204557685910100
2.5847-2.6680.24771500.207357785928100
2.668-2.76310.24891360.202357565892100
2.7631-2.87340.26681340.183158145948100
2.8734-3.00370.25871540.177557565910100
3.0037-3.16150.22341640.170857805944100
3.1615-3.35870.23061570.170457845941100
3.3587-3.61650.21541360.149258155951100
3.6165-3.97780.18491510.143457945945100
3.9778-4.54730.18891420.128258265968100
4.5473-5.70610.15651440.123658425986100
5.7061-19.76490.16191560.138359336089100
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)
11.77510.9417-0.48681.5694-0.73951.0911-0.07040.1139-0.3659-0.1209-0.00160.07890.4431-0.15070.09370.6229-0.0416-0.03320.4042-0.11370.6307-24.011813.3679108.0909
22.30120.20840.02734.05460.21684.38820.0158-0.335-0.31880.4037-0.0434-0.47220.42220.32440.09610.45740.0301-0.01680.3614-0.02260.5178-17.921822.2887121.4301
32.9355-1.0690.09143.23621.30334.3545-0.00310.66540.104-0.7526-0.1564-0.1551-0.12620.03510.17030.62730.03160.06820.56670.02080.403-0.171339.742984.3217
43.74690.686-0.53541.7003-0.02721.1691-0.03080.3181-0.0641-0.3269-0.0525-0.08560.0803-0.03430.06890.53170.0427-0.03470.4053-0.06360.4366-11.180130.558796.7952
53.1132-0.16330.08461.98-0.1311.9293-0.0440.46640.208-0.5089-0.02430.0451-0.0581-0.25640.01380.46780.0262-0.1190.392-0.01670.3277-18.65345.558294.5986
61.45110.7995-0.45212.2988-0.26731.19810.108-0.11220.37970.1321-0.09710.1466-0.3029-0.0147-0.01580.46380.0143-0.06290.3581-0.06330.603-14.49262.6622115.359
72.7958-0.49570.22843.425-0.1161.6490.031-0.17110.20780.3913-0.1682-0.4079-0.06970.29360.21520.4778-0.0141-0.11170.3444-0.01120.4384-4.619948.7317114.1142
81.52220.3817-0.38361.4009-0.55691.76480.0303-0.24620.14510.4797-0.03750.4013-0.161-0.424-0.03910.569-0.01830.07020.551-0.12490.5558-34.22841.2264132.0576
92.78460.62330.42942.6107-0.08615.5290.02410.10330.020.02850.10550.6585-0.3913-0.7965-0.06840.44320.03310.00470.4858-0.0780.6099-37.204335.5629116.3198
105.1107-0.2844-0.66255.6518-2.59784.7587-0.6752-0.5533-1.0671-0.39250.4067-0.17860.93670.39260.29720.96250.15630.16370.62950.12070.7566-41.28739.72360.5655
115.51411.0923-1.79466.8812-1.56935.3581-0.1343-0.2007-1.1032-0.8950.29070.56010.6937-0.5821-0.08651.13380.01440.03130.65070.28390.972-47.7043.463967.053
123.6963-0.93490.51473.2643-0.67441.6951-0.0874-0.441-0.55450.27850.10050.12920.3404-0.0108-0.07360.79660.06590.08920.61990.12370.5012-49.995121.994769.9579
131.4551-1.5259-1.32656.0671-0.42281.98060.7622-1.2482-1.0861-0.1312-0.40360.81581.5401-0.9697-0.14820.8818-0.10350.06840.68420.21160.8402-50.758719.477957.6732
148.0496-2.01620.65065.10781.95052.7246-0.8366-0.4791-0.6516-0.31350.07761.13561.6215-1.42630.54591.1216-0.2748-0.01951.0267-0.07480.8622-61.339620.199444.5922
155.29720.47574.05464.9917-1.30597.9484-0.50620.3021-0.3451-0.06630.2217-0.09080.34990.39960.22170.39220.04690.15710.31720.04920.3097-43.079122.648354.3651
162.98390.4747-2.15056.8471.20291.9693-0.39850.1144-0.5716-1.11670.0218-1.64960.63361.21810.17071.02120.09260.19990.9093-0.01280.75-29.501822.010340.0579
175.6132-4.08761.68295.08791.8765.0624-0.29820.2571-0.0329-0.0958-0.1104-0.69880.43511.4228-1.710.54030.13030.27890.84340.00740.6976-23.208427.459840.9718
186.8664-2.45161.8715.26190.75572.16170.17730.8882-0.1408-0.8968-0.3336-0.3393-0.63271.26970.12050.85220.05710.45051.3219-0.04660.8472-18.801128.928135.0569
192.2658-0.4579-0.00892.53460.86794.0499-0.11310.374-0.0693-0.73320.0741-0.4720.23140.5119-0.05220.68320.01380.12050.63980.04970.4554-35.978438.700139.4711
206.71422.69034.13937.38993.20935.3808-0.5236-0.18540.30040.00220.1289-1.0122-0.33630.56390.31720.39090.00110.0110.74370.14330.6643-26.377837.084158.8047
215.7094-0.71830.81541.410.53187.03170.1210.364-0.6948-0.2982-0.1197-0.16220.64560.27260.00570.4260.02870.0670.33510.06550.3768-36.141227.608652.5527
227.60950.3788-3.73872.3992-1.94277.1865-0.3012-0.36310.44180.1370.39430.1881-0.33030.48740.01510.88890.0643-0.10610.48510.04090.539-56.431467.932453.0982
238.6462-0.3373-0.41045.701-2.21734.1714-0.07850.20810.3556-0.33080.22990.4429-0.2855-0.4045-0.16730.76360.0561-0.070.52220.08930.4607-57.57469.720842.2683
241.9806-0.17030.27574.53570.42542.0572-0.09710.18230.1671-0.38350.1219-0.0503-0.24470.0884-0.06040.6292-0.0415-0.01310.58270.08550.3423-45.063656.540145.2931
253.3345-1.8684-2.15962.7911-0.86863.8757-0.46830.76890.3565-1.05540.52591.0626-0.4278-0.25220.21710.8477-0.0846-0.19790.55640.16690.5657-56.933853.350546.843
262.137-0.1961.05077.022.2982.058-0.57430.4791-1.0332-0.97590.5526-0.0249-0.4295-0.1815-0.10731.1751-0.0914-0.11750.90190.07510.8948-67.580341.055936.9594
273.48271.1875-0.02192.5829-1.68721.2951-0.1431-0.07010.24630.09190.36310.2742-0.1477-0.2422-0.19090.5010.0888-0.01590.54550.05160.3022-60.670150.851553.7788
282.6872.4417-1.56333.169-1.62245.07680.0581-0.62180.18330.54260.17470.66990.13190.0698-0.26580.99110.28580.21250.90560.00820.6163-67.904353.671675.8777
293.582-0.2744-1.03592.11932.30882.6687-0.157-0.7154-0.35381.410.15380.4172-0.2513-0.260.32221.5910.44010.26551.07750.07260.6115-70.462651.833384.5508
300.50450.2562-0.42871.39270.41280.9688-0.1068-0.5023-0.14110.76680.23620.4338-0.0559-0.342-0.10370.75290.15870.17770.74150.13630.4588-63.133438.029372.3378
310.68620.7351.93633.46420.28716.6307-0.1415-1.25880.17960.8688-0.05570.1391-0.36210.0555-0.00020.79150.1317-0.06090.7771-0.0070.2915-46.135251.583574.9919
325.26920.9669-2.87882.968-0.69772.6983-0.2358-0.42880.26820.63890.25420.2504-0.4824-0.0028-0.0090.73440.11630.0480.66280.03670.4258-56.946551.821864.3626
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 180 )
2X-RAY DIFFRACTION2chain 'A' and (resid 181 through 254 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 92 )
4X-RAY DIFFRACTION4chain 'B' and (resid 93 through 180 )
5X-RAY DIFFRACTION5chain 'B' and (resid 181 through 254 )
6X-RAY DIFFRACTION6chain 'C' and (resid 2 through 180 )
7X-RAY DIFFRACTION7chain 'C' and (resid 181 through 254 )
8X-RAY DIFFRACTION8chain 'D' and (resid 2 through 180 )
9X-RAY DIFFRACTION9chain 'D' and (resid 181 through 254 )
10X-RAY DIFFRACTION10chain 'E' and (resid 2 through 30 )
11X-RAY DIFFRACTION11chain 'E' and (resid 31 through 69 )
12X-RAY DIFFRACTION12chain 'E' and (resid 70 through 180 )
13X-RAY DIFFRACTION13chain 'E' and (resid 181 through 197 )
14X-RAY DIFFRACTION14chain 'E' and (resid 198 through 220 )
15X-RAY DIFFRACTION15chain 'E' and (resid 221 through 254 )
16X-RAY DIFFRACTION16chain 'F' and (resid 2 through 18 )
17X-RAY DIFFRACTION17chain 'F' and (resid 19 through 41 )
18X-RAY DIFFRACTION18chain 'F' and (resid 42 through 69 )
19X-RAY DIFFRACTION19chain 'F' and (resid 70 through 180 )
20X-RAY DIFFRACTION20chain 'F' and (resid 181 through 220 )
21X-RAY DIFFRACTION21chain 'F' and (resid 221 through 254 )
22X-RAY DIFFRACTION22chain 'G' and (resid 2 through 18 )
23X-RAY DIFFRACTION23chain 'G' and (resid 19 through 69 )
24X-RAY DIFFRACTION24chain 'G' and (resid 70 through 180 )
25X-RAY DIFFRACTION25chain 'G' and (resid 181 through 197 )
26X-RAY DIFFRACTION26chain 'G' and (resid 198 through 211 )
27X-RAY DIFFRACTION27chain 'G' and (resid 212 through 254 )
28X-RAY DIFFRACTION28chain 'H' and (resid 2 through 42 )
29X-RAY DIFFRACTION29chain 'H' and (resid 43 through 69 )
30X-RAY DIFFRACTION30chain 'H' and (resid 70 through 180 )
31X-RAY DIFFRACTION31chain 'H' and (resid 181 through 220 )
32X-RAY DIFFRACTION32chain 'H' and (resid 221 through 254 )

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