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- PDB-4weo: Crystal Structure of a Putative acetoin(Diacetyl) Reductase Burkh... -

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Basic information

Entry
Database: PDB / ID: 4weo
TitleCrystal Structure of a Putative acetoin(Diacetyl) Reductase Burkholderia cenocepacia
ComponentsPutative acetoin(Diacetyl) reductase
KeywordsOXIDOREDUCTASE / SSGCID / Burkholderia cenocepacia / reductase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


acetoin dehydrogenase / oxidoreductase activity
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
Putative acetoin(Diacetyl) reductase
Similarity search - Component
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Putative acetoin(Diacetyl) Reductase Burkholderia cenocepacia
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Dranow, D.M. / Fairman, J.W. / Lorimer, D. / Edwards, T.E.
History
DepositionSep 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 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 / refine_hist / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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_symmetry / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative acetoin(Diacetyl) reductase
B: Putative acetoin(Diacetyl) reductase
C: Putative acetoin(Diacetyl) reductase
D: Putative acetoin(Diacetyl) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,99817
Polymers113,2334
Non-polymers76513
Water13,511750
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14630 Å2
ΔGint-45 kcal/mol
Surface area29180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.710, 85.490, 76.520
Angle α, β, γ (deg.)90.00, 92.27, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-408-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B
311CHAIN C
411CHAIN D

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative acetoin(Diacetyl) reductase


Mass: 28308.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria)
Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610
Gene: budC, BCAL1912 / Plasmid: BuceA.00010.q.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4EAZ8, acetoin dehydrogenase

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Non-polymers , 5 types, 763 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 750 / 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: 2.25 Å3/Da / Density % sol: 45.26 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: JCSG+(B8): 10% PEG-8000, 0.1M Tris base/HCl, pH=7.0, 0.2M MgCl2, cryo protected with 25% EG; BuceA.00010.q.B1.PS01731 at 19.4 mg/ml, tray 24028
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97624 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 21, 2014 / Details: Bimorph K-B pair
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 84056 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 15.54 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 13.57
Reflection shellResolution: 1.85→1.9 Å / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 2.92 / % possible all: 97.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1769)refinement
XDSdata reduction
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UVD
Resolution: 1.85→37.46 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 18.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.19 3750 4.66 %
Rwork0.154 --
obs0.156 80438 94.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.13 Å2
Refinement stepCycle: LAST / Resolution: 1.85→37.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6889 0 47 750 7686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077049
X-RAY DIFFRACTIONf_angle_d0.9619572
X-RAY DIFFRACTIONf_dihedral_angle_d11.922444
X-RAY DIFFRACTIONf_chiral_restr0.0421154
X-RAY DIFFRACTIONf_plane_restr0.0051261
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A4171X-RAY DIFFRACTIONPOSITIONAL
12B4171X-RAY DIFFRACTIONPOSITIONAL
13C4171X-RAY DIFFRACTIONPOSITIONAL
14D4171X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.87350.26071130.19622521X-RAY DIFFRACTION85
1.8735-1.89810.25681640.20722567X-RAY DIFFRACTION86
1.8981-1.92410.22561270.18962584X-RAY DIFFRACTION87
1.9241-1.95160.25451480.18732651X-RAY DIFFRACTION89
1.9516-1.98070.21311270.18142668X-RAY DIFFRACTION89
1.9807-2.01170.23061320.17142737X-RAY DIFFRACTION90
2.0117-2.04470.20051300.16572727X-RAY DIFFRACTION92
2.0447-2.07990.1914920.16352812X-RAY DIFFRACTION92
2.0799-2.11780.2021250.16222809X-RAY DIFFRACTION93
2.1178-2.15850.19631370.16052813X-RAY DIFFRACTION94
2.1585-2.20250.21141290.15012859X-RAY DIFFRACTION94
2.2025-2.25040.21541120.15182895X-RAY DIFFRACTION95
2.2504-2.30280.19421330.14722846X-RAY DIFFRACTION95
2.3028-2.36030.17641380.15092870X-RAY DIFFRACTION95
2.3603-2.42410.21041130.15282893X-RAY DIFFRACTION96
2.4241-2.49550.21541470.14772883X-RAY DIFFRACTION95
2.4955-2.5760.18311400.152899X-RAY DIFFRACTION97
2.576-2.6680.18131350.14922949X-RAY DIFFRACTION97
2.668-2.77480.18841410.15812950X-RAY DIFFRACTION97
2.7748-2.90110.20261470.15682909X-RAY DIFFRACTION98
2.9011-3.0540.2141520.15352989X-RAY DIFFRACTION98
3.054-3.24520.1651310.15282943X-RAY DIFFRACTION98
3.2452-3.49560.17611860.14572956X-RAY DIFFRACTION98
3.4956-3.84710.17271750.1332989X-RAY DIFFRACTION99
3.8471-4.4030.17731440.13612984X-RAY DIFFRACTION98
4.403-5.54440.16651700.14192985X-RAY DIFFRACTION99
5.5444-37.470.16491620.17063000X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.75950.31590.43973.1087-0.48893.1765-0.1071-0.13380.38060.03870.05650.1706-0.1993-0.27280.02160.16570.0632-0.03740.1427-0.04330.23349.812725.815917.3389
21.1664-0.1997-0.18654.228-0.41021.45150.086-0.03720.18330.4378-0.02590.6734-0.2829-0.37590.19460.35350.1764-0.04260.3913-0.21550.49263.188931.558523.0724
33.60613.9530.11218.02560.54440.8449-0.0068-0.23010.5202-0.4473-0.13490.7373-0.1958-0.1930.08690.20070.0909-0.03540.2549-0.02880.2921.103623.583615.6087
41.1198-0.1554-0.08421.1262-0.26730.9544-0.1064-0.11320.14450.11380.04270.2005-0.1655-0.26570.04280.13220.0325-0.01260.1918-0.05010.19933.621614.294817.2148
50.62950.7853-0.71953.9224-3.52515.28530.0269-0.0170.04070.0473-0.00210.2381-0.1841-0.2265-0.04030.08270.0262-0.02220.1855-0.02480.20634.56148.852813.0546
60.5570.06030.29091.5275-1.40244.43020.0187-0.02020.01280.0798-0.00230.1128-0.1015-0.0229-0.02510.05060.00660.00350.0963-0.00280.106314.38616.775517.8634
71.23320.37571.15091.20960.25311.81320.0652-0.15160.07050.134-0.06830.1175-0.0122-0.2563-0.02490.1120.0020.00930.1371-0.02220.130819.277414.717924.0973
81.76380.11030.54870.7371-0.22978.4620.018-0.04010.03450.0674-0.0057-0.0183-0.0092-0.1507-0.04950.0724-0.0122-0.01120.0764-0.02120.115624.517111.152618.2872
91.7928-0.0579-1.08453.5991-0.41492.06910.03590.0817-0.54890.03560.0130.17870.3653-0.288-0.05180.2238-0.0977-0.00730.16560.00030.27439.9261-25.864318.4081
102.2447-2.1037-0.99752.30180.38741.35540.15970.2469-0.7548-0.83620.08190.73510.509-0.5831-0.14760.4621-0.2226-0.04630.3723-0.0760.49594.2726-31.861512.0515
112.8373-2.27580.3862.26250.22131.3504-0.1644-0.0135-0.66720.41190.11830.80180.3667-0.54140.03340.2618-0.14360.0620.363-0.02170.36011.0667-23.714819.329
121.12270.46580.04111.1889-0.06280.5546-0.0479-0.0649-0.2062-0.06030.03960.20360.2808-0.4431-0.00890.1737-0.07180.03120.2534-0.02270.2453.6387-14.402917.9797
131.7001-1.15030.97734.1748-3.29424.58670.0437-0.1386-0.10770.14870.03140.38060.0572-0.2852-0.10950.1145-0.05280.01950.2172-0.0150.19774.0165-8.857521.8938
141.25250.7287-1.27993.8512-3.90496.9091-0.0227-0.0613-0.0641-0.085-0.0809-0.01680.2511-0.00530.13410.0977-0.00280.00090.1041-0.01180.103615.7235-8.588915.7502
151.5354-0.8267-0.19451.7827-0.43140.943-0.0011-0.1625-0.06010.10090.04930.19150.1446-0.0338-0.05560.0886-0.03380.01250.1038-0.00230.121814.587-7.77123.3467
164.6687-4.0851.79764.9765-3.24875.60990.45080.61320.0038-0.5824-0.31050.40460.0758-1.2359-0.04560.30720.0653-0.0420.4204-0.09280.216817.7378-10.0928-0.5362
171.616-0.0119-0.86751.12770.12965.14780.02150.0287-0.0673-0.0493-0.00230.05170.1998-0.2217-0.01820.07540.0078-0.00180.08040.00070.114223.3367-15.718415.0783
182.0164-0.59490.21721.4404-0.71462.21430.0311-0.0418-0.09420.0366-0.0102-0.03820.18580.1315-0.02850.15710.03480.00480.0820.01340.101744.0989-27.046525.0461
191.72162.297-0.60326.3505-1.40221.3649-0.0790.0584-0.25630.0327-0.0124-0.72590.22770.24030.05260.18730.06330.00330.14850.02150.144351.5562-23.429221.8935
200.7451-0.4453-0.06923.00631.3521.2847-0.00510.0449-0.03090.11290.0281-0.16640.16330.1949-0.03270.11370.0166-0.00190.13910.03410.107648.5379-11.932619.3358
211.2306-1.456-1.5191.75382.17525.276-0.05050.0441-0.04390.189-0.10660.1660.1651-0.04560.1570.0952-0.02830.00160.10060.02040.099936.562-8.760122.2717
220.70090.37390.31181.10781.00031.4050.02030.0735-0.04010.0265-0.0141-0.02080.12420.0657-0.00110.09870.014-0.00440.07990.01250.090237.8018-8.455815.2372
235.753.33171.73756.53461.98147.38540.3181-0.63370.45781.0198-0.2578-0.3175-0.37340.6554-0.0890.4151-0.0952-0.0210.3666-0.0030.267935.3038-7.282139.8863
241.2391-0.606-0.58841.59780.42993.265-0.0278-0.0328-0.03110.15430.00950.0390.1218-0.0360.02190.0885-0.0211-0.00130.07660.01330.105228.9798-14.834524.362
254.08420.52590.7012.1142-1.37783.49230.0369-0.12590.29080.10270.0192-0.0591-0.22570.0706-0.08810.1308-0.0663-0.02290.06970.02810.105541.672525.829718.3658
262.3202-0.2259-0.53761.7717-0.06322.761-0.02130.04840.08370.01740.0221-0.0499-0.16360.18060.0090.1666-0.041-0.01370.10330.01420.116445.690627.205811.6438
273.0015-2.65110.95977.1105-1.64531.7885-0.0771-0.0710.15940.26830.0499-0.5687-0.19820.24160.01120.1657-0.0718-0.01260.16980.01520.110151.591223.516917.4457
281.00560.3333-0.03792.19670.14330.4014-0.0109-0.04690.0532-0.1438-0.0162-0.1245-0.21070.14980.01780.1329-0.02860.00090.14790.03140.091748.806914.274117.5608
290.707-0.1003-0.11811.14610.66041.52390.0258-0.03340.00360.0212-0.0542-0.0401-0.0630.04070.01790.0983-0.0102-0.0060.08520.01950.08841.23728.8320.9927
307.63462.44131.23786.3281-1.17873.18980.13130.6507-0.5305-0.6788-0.2291-0.45320.3610.7268-0.00510.36490.0698-0.0040.3110.00470.229737.597.2989-1.9687
311.25510.45630.50841.3260.87474.68320.05840.07590.0086-0.1180.0335-0.0453-0.147-0.0651-0.0520.11040.0053-0.00150.06770.01120.104330.646818.04259.8194
322.01360.23510.76780.0879-0.3465.45060.0244-0.0535-0.0264-0.016-0.00750.0272-0.0556-0.061-0.02570.07450.0109-0.00550.05740.00960.096327.870711.036217.1461
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 3 THROUGH 40 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 41 THROUGH 54 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 55 THROUGH 67 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 68 THROUGH 104 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 105 THROUGH 133 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 134 THROUGH 173 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 174 THROUGH 240 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 241 THROUGH 258 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 3 THROUGH 40 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 41 THROUGH 54 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 55 THROUGH 67 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 68 THROUGH 104 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 105 THROUGH 133 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 134 THROUGH 153 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 154 THROUGH 186 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 187 THROUGH 219 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 220 THROUGH 258 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 3 THROUGH 54 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 55 THROUGH 67 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 68 THROUGH 133 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 134 THROUGH 153 )
22X-RAY DIFFRACTION22CHAIN 'C' AND (RESID 154 THROUGH 186 )
23X-RAY DIFFRACTION23CHAIN 'C' AND (RESID 187 THROUGH 219 )
24X-RAY DIFFRACTION24CHAIN 'C' AND (RESID 220 THROUGH 258 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 3 THROUGH 17 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 18 THROUGH 54 )
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESID 55 THROUGH 67 )
28X-RAY DIFFRACTION28CHAIN 'D' AND (RESID 68 THROUGH 104 )
29X-RAY DIFFRACTION29CHAIN 'D' AND (RESID 105 THROUGH 186 )
30X-RAY DIFFRACTION30CHAIN 'D' AND (RESID 187 THROUGH 219 )
31X-RAY DIFFRACTION31CHAIN 'D' AND (RESID 220 THROUGH 240 )
32X-RAY DIFFRACTION32CHAIN 'D' AND (RESID 241 THROUGH 258 )

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