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- PDB-4ueo: Open state of galactitol-1-phosphate 5-dehydrogenase from E. coli... -

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Basic information

Entry
Database: PDB / ID: 4ueo
TitleOpen state of galactitol-1-phosphate 5-dehydrogenase from E. coli, with zinc in the catalytic site.
ComponentsGALACTITOL-1-PHOSPHATE 5-DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


galactitol-1-phosphate 5-dehydrogenase / galactitol-1-phosphate 5-dehydrogenase activity / galactitol catabolic process / protein homodimerization activity / zinc ion binding / identical protein binding / cytosol
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 / Polyketide synthase, enoylreductase domain / Enoylreductase ...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 / Polyketide synthase, enoylreductase domain / Enoylreductase / 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
Galactitol 1-phosphate 5-dehydrogenase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBenavente, R. / Esteban-Torres, M. / Kohring, G.W. / Cortes-Cabrera, A. / Gago, F. / Acebron, I. / de las Rivas, B. / Munoz, R. / Mancheno, J.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Enantioselective Oxidation of Galactitol 1-Phosphate by Galactitol-1-Phosphate 5-Dehydrogenase from Escherichia Coli
Authors: Benavente, R. / Esteban-Torres, M. / Kohring, G.W. / Cortes-Cabrera, A. / Sanchez-Murcia, P.A. / Gago, F. / Acebron, I. / De Las Rivas, B. / Munoz, R. / Mancheno, J.M.
History
DepositionDec 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _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_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_label_seq_id / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: GALACTITOL-1-PHOSPHATE 5-DEHYDROGENASE
B: GALACTITOL-1-PHOSPHATE 5-DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1877
Polymers74,8602
Non-polymers3275
Water4,972276
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3720 Å2
ΔGint-97.5 kcal/mol
Surface area27860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.306, 76.906, 108.651
Angle α, β, γ (deg.)90.00, 95.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein GALACTITOL-1-PHOSPHATE 5-DEHYDROGENASE /


Mass: 37430.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P0A9S3, galactitol-1-phosphate 5-dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.2 Å3/Da / Density % sol: 46 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.28245
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28245 Å / Relative weight: 1
ReflectionResolution: 2→44.23 Å / Num. obs: 47058 / % possible obs: 97.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 33.47 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.8 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A2C

4a2c


Resolution: 2→44.235 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 30.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2558 2376 5.1 %
Rwork0.1943 --
obs0.1975 46912 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→44.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5254 0 5 276 5535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095364
X-RAY DIFFRACTIONf_angle_d1.4097278
X-RAY DIFFRACTIONf_dihedral_angle_d13.6081952
X-RAY DIFFRACTIONf_chiral_restr0.057838
X-RAY DIFFRACTIONf_plane_restr0.007940
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.04080.3821310.30892580X-RAY DIFFRACTION95
2.0408-2.08520.32191230.27992558X-RAY DIFFRACTION96
2.0852-2.13370.3311260.25452597X-RAY DIFFRACTION96
2.1337-2.18710.27191590.23722576X-RAY DIFFRACTION97
2.1871-2.24620.41061200.30652485X-RAY DIFFRACTION93
2.2462-2.31230.2851230.22422615X-RAY DIFFRACTION97
2.3123-2.38690.26811370.21462616X-RAY DIFFRACTION97
2.3869-2.47220.2951370.21722600X-RAY DIFFRACTION97
2.4722-2.57120.27961580.20772602X-RAY DIFFRACTION98
2.5712-2.68820.28851220.20232647X-RAY DIFFRACTION98
2.6882-2.82990.24671430.20372629X-RAY DIFFRACTION98
2.8299-3.00720.251460.20532617X-RAY DIFFRACTION99
3.0072-3.23930.25871550.19692630X-RAY DIFFRACTION98
3.2393-3.56510.2441570.18062661X-RAY DIFFRACTION99
3.5651-4.08070.22031500.16812648X-RAY DIFFRACTION99
4.0807-5.140.22391560.14942703X-RAY DIFFRACTION100
5.14-44.24530.24181330.18492772X-RAY DIFFRACTION100
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)
15.81260.9339-0.42966.23963.48574.97190.1094-0.3009-0.14-0.05340.2146-1.0658-0.06620.6096-0.2640.39790.03420.04480.3615-0.00570.442425.379-6.5505-4.3446
20.6034-0.2934-1.52372.91671.56573.9004-0.0790.0662-0.2502-0.1752-0.1179-0.04950.11350.03740.17460.21610.0284-0.02560.2632-0.01830.240512.8306-4.16355.3014
30.96520.7463-0.96822.4325-0.38293.43660.1499-0.1477-0.0510.2099-0.2502-0.0071-0.24820.24260.08750.2105-0.01090.02440.26560.00350.248512.77314.756720.6682
46.7526-1.4750.65546.4077-0.52721.529-0.12730.4265-1.0947-0.08040.4998-1.93760.0721.1778-0.47230.6651-0.12830.27430.5655-0.27521.310431.80596.36013.0294
51.4023-2.274-1.8614.88642.24963.4792-0.6668-0.74230.32381.33690.9612-0.72510.55850.7464-0.19180.72570.095-0.02160.5506-0.15490.5101-4.2622-10.248662.6043
63.4303-4.0187-2.55466.58060.29415.548-0.2864-0.55220.16730.7209-0.0522-0.27240.17720.65330.36380.4637-0.02990.07010.4017-0.00140.3864-9.3019-7.617356.878
72.40710.0191-3.51334.5822-2.31267.62140.0583-0.06560.03990.4161-0.0643-0.1235-0.35990.1190.00330.2975-0.03220.05180.3275-0.05590.3158-7.9683-7.66247.2457
81.58130.1466-1.38261.9878-0.9392.6209-0.1506-0.1769-0.21910.0774-0.1791-0.06550.29870.18380.30910.3422-0.00350.09260.26880.01770.28654.6355-20.63433.9741
91.43740.25062.38073.86622.54635.1425-0.4226-0.8287-0.16171.99170.9355-0.83350.51841.5594-0.27341.10690.3921-0.06080.8543-0.06620.54672.0467-22.899960.3453
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 79 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 80 THROUGH 183 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 184 THROUGH 322 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 323 THROUGH 346 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 1 THROUGH 46 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 47 THROUGH 79 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 80 THROUGH 155 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 156 THROUGH 322 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 323 THROUGH 346 )

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