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- PDB-5je8: The crystal structure of Bacillus cereus 3-hydroxyisobutyrate deh... -

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Basic information

Entry
Database: PDB / ID: 5je8
TitleThe crystal structure of Bacillus cereus 3-hydroxyisobutyrate dehydrogenase in complex with NAD
Components3-hydroxyisobutyrate dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase
Function / homology
Function and homology information


3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase activity / organic acid catabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding
Similarity search - Function
3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 ...3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-hydroxyisobutyrate dehydrogenase
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPark, S.C. / Yoon, S.I.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Structural and biochemical characterization of the Bacillus cereus 3-hydroxyisobutyrate dehydrogenase
Authors: Park, S.C. / Kim, P.H. / Lee, G.S. / Kang, S.G. / Ko, H.J. / Yoon, S.I.
History
DepositionApr 18, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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: 3-hydroxyisobutyrate dehydrogenase
B: 3-hydroxyisobutyrate dehydrogenase
C: 3-hydroxyisobutyrate dehydrogenase
D: 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,18911
Polymers131,1134
Non-polymers3,0767
Water10,106561
1
A: 3-hydroxyisobutyrate dehydrogenase
B: 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2146
Polymers65,5562
Non-polymers1,6574
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8560 Å2
ΔGint-55 kcal/mol
Surface area21880 Å2
2
C: 3-hydroxyisobutyrate dehydrogenase
D: 3-hydroxyisobutyrate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9755
Polymers65,5562
Non-polymers1,4193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-67 kcal/mol
Surface area22240 Å2
Unit cell
Length a, b, c (Å)46.444, 158.576, 163.138
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D

NCS domain segments:

Refine code: 5

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSLYSLYSAA3 - 1729 - 178
221LYSLYSLYSLYSBB3 - 1729 - 178
331LYSLYSLYSLYSCC3 - 1729 - 178
441LYSLYSLYSLYSDD3 - 1729 - 178
112LEULEUGLNGLNAA173 - 290179 - 296
222LEULEUGLNGLNBB173 - 290179 - 296
332LEULEUGLNGLNCC173 - 290179 - 296
442LEULEUGLNGLNDD173 - 290179 - 296
113NADNADNADNADAE401
223NADNADNADNADBG401
333NADNADNADNADCI401
443NADNADNADNADDJ401

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
3-hydroxyisobutyrate dehydrogenase


Mass: 32778.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Strain: ATCC 14579 / Gene: BC_2289 / Production host: Escherichia coli (E. coli)
References: UniProt: Q81DR6, 3-hydroxyisobutyrate dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 22% PEG 6000, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00001 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 72368 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 27.6
Reflection shellResolution: 2.1→2.18 Å

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CKY

3cky


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.927 / Cross valid method: THROUGHOUT / ESU R: 0.242 / ESU R Free: 0.196 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24269 3585 5 %RANDOM
Rwork0.1973 ---
obs0.19959 67647 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20 Å2
2---0.53 Å20 Å2
3----0.31 Å2
Refinement stepCycle: 1 / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8807 0 203 561 9571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0229211
X-RAY DIFFRACTIONr_bond_other_d00.026043
X-RAY DIFFRACTIONr_angle_refined_deg1.4832.00312483
X-RAY DIFFRACTIONr_angle_other_deg4.284314915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93651174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.63125.978368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.605151572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6391516
X-RAY DIFFRACTIONr_chiral_restr0.0880.21431
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210189
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021751
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6131.55769
X-RAY DIFFRACTIONr_mcbond_other01.52409
X-RAY DIFFRACTIONr_mcangle_it1.01229237
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.89233442
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.0084.53240
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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
1A993MEDIUM POSITIONAL0.310.5
1B993MEDIUM POSITIONAL0.160.5
1C993MEDIUM POSITIONAL0.190.5
1D993MEDIUM POSITIONAL0.240.5
1A1042LOOSE POSITIONAL0.675
1B1042LOOSE POSITIONAL0.455
1C1042LOOSE POSITIONAL0.535
1D1042LOOSE POSITIONAL0.595
1A993MEDIUM THERMAL0.142
1B993MEDIUM THERMAL0.182
1C993MEDIUM THERMAL0.082
1D993MEDIUM THERMAL0.142
1A1042LOOSE THERMAL0.5210
1B1042LOOSE THERMAL0.5910
1C1042LOOSE THERMAL0.4210
1D1042LOOSE THERMAL0.4410
2A700MEDIUM POSITIONAL0.170.5
2B700MEDIUM POSITIONAL0.160.5
2C700MEDIUM POSITIONAL0.220.5
2D700MEDIUM POSITIONAL0.180.5
2A788LOOSE POSITIONAL0.445
2B788LOOSE POSITIONAL0.355
2C788LOOSE POSITIONAL0.435
2D788LOOSE POSITIONAL0.385
2A700MEDIUM THERMAL4.062
2B700MEDIUM THERMAL4.652
2C700MEDIUM THERMAL2.522
2D700MEDIUM THERMAL10.922
2A788LOOSE THERMAL3.6510
2B788LOOSE THERMAL4.1410
2C788LOOSE THERMAL2.5110
2D788LOOSE THERMAL9.910
3A66LOOSE POSITIONAL0.235
3B66LOOSE POSITIONAL0.185
3C66LOOSE POSITIONAL0.175
3D66LOOSE POSITIONAL0.175
3A66LOOSE THERMAL10.0710
3B66LOOSE THERMAL3.5910
3C66LOOSE THERMAL13.1810
3D66LOOSE THERMAL6.6710
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 251 -
Rwork0.253 4898 -
obs--99.67 %
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)
13.04971.1537-0.40442.4799-0.81281.52720.1025-0.21850.1410.1742-0.06730.2478-0.0722-0.0101-0.03510.2150.00940.00170.2149-0.0050.315216.77857.56323.133
21.06070.1728-0.622.91510.01921.1860.1193-0.08160.0910.1732-0.117-0.5535-0.10260.1498-0.00220.1181-0.0136-0.03250.18270.04880.390724.50829.67318.418
31.93280.39290.7311.8453-0.03971.73130.04820.0813-0.1073-0.11830.0149-0.12610.21710.0439-0.06320.24980.0240.03920.20150.01530.302815.7771.988-4.258
41.6230.0838-0.26682.5775-0.17040.93050.0560.09410.03010.0303-0.10560.0650.0307-0.05410.04960.1201-0.0047-0.00320.1708-0.01290.26699.79222.4517.806
51.729-0.4076-0.2897.8094-2.27184.0087-0.1981-0.0730.0089-0.08310.1282-0.21880.2198-0.07230.06980.4293-0.10360.0290.2591-0.01610.34522.501-46.58514.128
61.1492-0.21841.05668.63072.49982.5695-0.1515-0.0216-0.06411.82320.293-0.90250.8944-0.0002-0.14150.83190.0532-0.15620.1203-0.00670.306214.422-21.68425.571
72.1591-0.5181-0.01752.97061.3364.01510.1452-0.15130.08380.7694-0.0697-0.0091.028-0.1394-0.07550.726-0.05780.02020.2391-0.00890.28586.2459.02344.629
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 172
2X-RAY DIFFRACTION2A173 - 291
3X-RAY DIFFRACTION3B-1 - 172
4X-RAY DIFFRACTION4B173 - 292
5X-RAY DIFFRACTION5C2 - 172
6X-RAY DIFFRACTION6C173 - 290
7X-RAY DIFFRACTION7D1 - 172

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