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- PDB-4uej: Closed state of galactitol-1-phosphate 5-dehydrogenase from E. co... -

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Basic information

Entry
Database: PDB / ID: 4uej
TitleClosed state of galactitol-1-phosphate 5-dehydrogenase from E. coli in complex with glycerol.
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 ...: / 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: 1.74 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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

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)75,3719
Polymers74,8602
Non-polymers5117
Water11,782654
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-118.7 kcal/mol
Surface area26640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.311, 78.810, 68.244
Angle α, β, γ (deg.)90.00, 94.75, 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 654 / 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: 45 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.96885
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96885 Å / Relative weight: 1
ReflectionResolution: 1.74→45.19 Å / Num. obs: 10144 / % possible obs: 99.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 15.58 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.2
Reflection shellResolution: 1.74→1.83 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.2 / % possible all: 99.2

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Processing

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

4a2c


Resolution: 1.74→41.672 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 25.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2281 3523 5 %
Rwork0.185 --
obs0.1872 69940 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→41.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5254 0 17 654 5925
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075482
X-RAY DIFFRACTIONf_angle_d1.1137457
X-RAY DIFFRACTIONf_dihedral_angle_d12.6242004
X-RAY DIFFRACTIONf_chiral_restr0.043859
X-RAY DIFFRACTIONf_plane_restr0.006967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.76380.29291460.2422644X-RAY DIFFRACTION98
1.7638-1.7890.28131340.23822631X-RAY DIFFRACTION98
1.789-1.81570.28861540.22672614X-RAY DIFFRACTION98
1.8157-1.84410.26541190.21952650X-RAY DIFFRACTION98
1.8441-1.87440.29341150.20612606X-RAY DIFFRACTION97
1.8744-1.90670.26251260.19822654X-RAY DIFFRACTION99
1.9067-1.94130.25131410.19782635X-RAY DIFFRACTION99
1.9413-1.97870.25911440.19322651X-RAY DIFFRACTION99
1.9787-2.01910.24821410.19332633X-RAY DIFFRACTION99
2.0191-2.0630.24051440.18062662X-RAY DIFFRACTION98
2.063-2.1110.2151350.18742623X-RAY DIFFRACTION99
2.111-2.16370.23661320.18512668X-RAY DIFFRACTION99
2.1637-2.22220.23641440.17332665X-RAY DIFFRACTION99
2.2222-2.28760.23121340.17562664X-RAY DIFFRACTION99
2.2876-2.36150.22731220.17842680X-RAY DIFFRACTION99
2.3615-2.44590.22271460.18692655X-RAY DIFFRACTION99
2.4459-2.54380.23171360.18462679X-RAY DIFFRACTION100
2.5438-2.65950.23171690.19742564X-RAY DIFFRACTION97
2.6595-2.79970.23741450.19442684X-RAY DIFFRACTION100
2.7997-2.97510.23691450.1892695X-RAY DIFFRACTION100
2.9751-3.20470.22081610.18572657X-RAY DIFFRACTION100
3.2047-3.52710.19981590.17452684X-RAY DIFFRACTION100
3.5271-4.03710.18981540.16242693X-RAY DIFFRACTION100
4.0371-5.08480.20231370.15692679X-RAY DIFFRACTION98
5.0848-41.68430.23351400.19432747X-RAY DIFFRACTION99
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)
12.6354-0.61870.54370.8226-0.14962.90730.06580.4346-0.3105-0.1731-0.00680.0590.24040.2572-0.02440.2402-0.00660.00610.2696-0.06850.175468.2749-2.030910.654
21.38410.0935-0.30220.73240.08923.17670.01470.205-0.0757-0.1630.0086-0.0176-0.08690.1851-0.01140.0986-0.00150.00710.0998-0.00570.119269.12733.34623.0025
32.11740.3859-0.29310.5961-0.39261.32560.0554-0.3156-0.36860.0432-0.0819-0.08560.15660.185-0.01610.0860.0147-0.00560.11520.04050.138863.931-4.708443.0176
42.254-0.4232-0.10041.18281.13412.05190.05480.3237-0.288-0.06460.0159-0.02540.25440.264-0.03020.18740.0456-0.0020.1677-0.0370.161774.5182-0.782822.724
52.1505-0.60470.44911.0389-0.2592.16320.01380.0939-0.1383-0.1228-0.02270.10020.1524-0.00370.02540.1626-0.01510.00820.0914-0.01040.101484.051337.531371.7712
60.47640.0845-0.42080.20140.29133.50710.0039-0.01760.0645-0.0859-0.01650.0106-0.12210.08980.01950.07550.00230.00530.06220.00790.10485.09443.042784.0647
72.4570.2598-0.21760.6932-0.28581.04820.0386-0.2828-0.27760.0329-0.0568-0.04670.11260.169500.08260.0150.00060.11850.02180.097680.137534.8263103.8899
83.2072-0.7211-0.03182.18670.83342.8050.0509-0.0562-0.0987-0.0054-0.0408-0.08250.10810.1326-0.01470.1125-0.00320.01010.11230.01980.059990.748238.816883.8136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 102 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 103 THROUGH 182 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 183 THROUGH 285 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 286 THROUGH 346 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 1 THROUGH 102 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 103 THROUGH 182 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 183 THROUGH 285 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 286 THROUGH 346 )

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