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- PDB-2h6e: Crystal structure of the D-arabinose dehydrogenase from Sulfolobu... -

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Basic information

Entry
Database: PDB / ID: 2h6e
TitleCrystal structure of the D-arabinose dehydrogenase from Sulfolobus solfataricus
ComponentsD-arabinose 1-dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / medium chain alcohol dehydrogenase
Function / homology
Function and homology information


alcohol dehydrogenase (NAD+) activity / alcohol dehydrogenase / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain ...Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alcohol dehydrogenase (Zn containing) (Adh-4)
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsBrouns, S.J.J. / Turnbull, A.P. / Akerboom, J. / Willemen, H.L.D.M. / De Vos, W.M. / Van der Oost, J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal Structure and Biochemical Properties of the d-Arabinose Dehydrogenase from Sulfolobus solfataricus
Authors: Brouns, S.J. / Turnbull, A.P. / Willemen, H.L. / Akerboom, J. / van der Oost, J.
History
DepositionMay 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-arabinose 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4663
Polymers37,3351
Non-polymers1312
Water3,873215
1
A: D-arabinose 1-dehydrogenase
hetero molecules

A: D-arabinose 1-dehydrogenase
hetero molecules

A: D-arabinose 1-dehydrogenase
hetero molecules

A: D-arabinose 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,86412
Polymers149,3414
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
MethodPQS
2
A: D-arabinose 1-dehydrogenase
hetero molecules

A: D-arabinose 1-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9326
Polymers74,6702
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area4010 Å2
ΔGint-91 kcal/mol
Surface area25130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.019, 84.019, 194.979
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: -y,-x,-z and -x,-y,z and y,x,-z

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Components

#1: Protein D-arabinose 1-dehydrogenase / E.C.1.1.1.117 / Adh-4


Mass: 37335.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: P2 / Gene: Adh-4 / Plasmid: pET24d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q97YM2, D-arabinose 1-dehydrogenase [NAD(P)+]
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.3 Å3/Da / Density % sol: 46.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.55
Details: 4 mg/ml protein, 0.1 M HEPES-NaOH, 10% v/v Jeffamine-600, pH 8.55, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.2827 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 19, 2005 / Details: mirrors
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2827 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 32525 / Num. obs: 32525 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.4 %
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 7 % / % possible all: 93

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
HKL-2000data reduction
SOLVEphasing
REFMAC5.2refinement
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.8→42 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.663 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23216 1642 5.1 %RANDOM
Rwork0.1949 ---
all0.19674 30781 --
obs0.19674 30781 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.344 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2--0.87 Å20 Å2
3----1.73 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2412 0 2 215 2629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222527
X-RAY DIFFRACTIONr_bond_other_d0.0010.021699
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9823435
X-RAY DIFFRACTIONr_angle_other_deg0.90334194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.7775342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.73924.94795
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.5615454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9431513
X-RAY DIFFRACTIONr_chiral_restr0.0820.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022826
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02471
X-RAY DIFFRACTIONr_nbd_refined0.1990.2493
X-RAY DIFFRACTIONr_nbd_other0.1850.21744
X-RAY DIFFRACTIONr_nbtor_refined0.170.21237
X-RAY DIFFRACTIONr_nbtor_other0.0840.21346
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2188
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1820.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.93531764
X-RAY DIFFRACTIONr_mcbond_other0.5483681
X-RAY DIFFRACTIONr_mcangle_it2.5152628
X-RAY DIFFRACTIONr_scbond_it4.5098972
X-RAY DIFFRACTIONr_scangle_it5.89511799
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 103 -
Rwork0.215 2060 -
obs--91.07 %
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)
18.06545.2064-13.362311.457-12.752824.2417-0.4447-1.0777-1.4431.31210.48321.3134-0.3895-0.5605-0.03850.1640.00450.01810.1692-0.14250.25270.4603-2.02945.3938
20.88070.4044-0.15725.1243-1.24653.3073-0.1010.26210.0543-0.99730.21880.5366-0.3219-0.2213-0.11780.2496-0.0187-0.06980.05320.09820.053347.168513.999511.1074
30.61150.24541.1024.54210.4071.98620.09210.25020.19770.3442-0.096-0.62370.23350.0030.0039-0.0203-0.0001-0.02790.00130.0260.013660.5259-2.611331.9972
44.0684-0.6042.185.2593-0.08133.8942-0.09360.19010.2267-0.11120.01450.03930.08510.22150.0791-0.0642-0.01190.0025-0.03820.0198-0.061547.2508-4.455128.9858
54.31241.9014-1.67533.5759-0.71391.2038-0.06950.4412-0.11940.2254-0.00160.96410.1323-0.40310.07110.0443-0.02970.02730.1454-0.08380.071617.3673-14.357133.6406
64.59073.89531.55246.20290.98125.3694-0.2133-0.16480.0236-0.3776-0.05780.13880.04290.01570.271-0.02730.0362-0.0098-0.00830.0513-0.031953.78474.380920.4759
73.0340.4333-1.83670.9434-0.38085.8086-0.16410.14320.04140.01060.04070.12190.14740.22530.1234-0.0712-0.0076-0.01840.01530.0497-0.021856.35830.080643.1135
81.665-0.27121.2242.86030.47423.4377-0.11450.11360.095-0.05580.10480.0322-0.15370.340.0097-0.1192-0.0381-0.02150.12310.0353-0.027365.19383.773846.615
91.95270.91070.33981.02160.12931.42830.0163-0.01690.11830.0458-0.00440.18070.2031-0.1014-0.0119-0.0791-0.0054-0.00230.00460.0141-0.022547.9628-5.155850.7107
100.2971-0.2690.36951.5213-1.46843.4423-0.1250.0372-0.03030.25110.24510.0162-0.1499-0.2723-0.12-0.04980.0227-0.00580.02480.0164-0.054148.3864-5.642250.2582
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 211 - 21
2X-RAY DIFFRACTION2AA22 - 7622 - 76
3X-RAY DIFFRACTION3AA77 - 9677 - 96
4X-RAY DIFFRACTION4AA97 - 10897 - 108
5X-RAY DIFFRACTION5AA109 - 126109 - 126
6X-RAY DIFFRACTION6AA127 - 144127 - 144
7X-RAY DIFFRACTION7AA145 - 172145 - 172
8X-RAY DIFFRACTION8AA173 - 204173 - 204
9X-RAY DIFFRACTION9AA205 - 268205 - 268
10X-RAY DIFFRACTION10AA269 - 344269 - 344

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