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- PDB-1kw1: Crystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase ... -

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Basic information

Entry
Database: PDB / ID: 1kw1
TitleCrystal Structure of 3-Keto-L-Gulonate 6-Phosphate Decarboxylase with bound L-gulonate 6-phosphate
Components3-Keto-L-Gulonate 6-Phosphate Decarboxylase
KeywordsLYASE / beta/alpha-barrel
Function / homology
Function and homology information


3-dehydro-L-gulonate-6-phosphate decarboxylase / 3-dehydro-L-gulonate-6-phosphate decarboxylase activity / L-ascorbic acid catabolic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' pyrimidine nucleobase biosynthetic process / magnesium ion binding
Similarity search - Function
3-keto-L-gulonate-6-phosphate decarboxylase, UlaD / HPS/KGPDC domain / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
L-GULURONIC ACID 6-PHOSPHATE / 3-keto-L-gulonate-6-phosphate decarboxylase UlaD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWise, E. / Yew, W.S. / Babbitt, P.C. / Gerlt, J.A. / Rayment, I.
CitationJournal: Biochemistry / Year: 2002
Title: Homologous (beta/alpha)8-barrel enzymes that catalyze unrelated reactions: orotidine 5'-monophosphate decarboxylase and 3-keto-L-gulonate 6-phosphate decarboxylase.
Authors: Wise, E. / Yew, W.S. / Babbitt, P.C. / Gerlt, J.A. / Rayment, I.
History
DepositionJan 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / 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_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.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: 3-Keto-L-Gulonate 6-Phosphate Decarboxylase
B: 3-Keto-L-Gulonate 6-Phosphate Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8076
Polymers47,2062
Non-polymers6014
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-64 kcal/mol
Surface area16150 Å2
MethodPISA
2
A: 3-Keto-L-Gulonate 6-Phosphate Decarboxylase
B: 3-Keto-L-Gulonate 6-Phosphate Decarboxylase
hetero molecules

A: 3-Keto-L-Gulonate 6-Phosphate Decarboxylase
B: 3-Keto-L-Gulonate 6-Phosphate Decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,61412
Polymers94,4124
Non-polymers1,2028
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area11290 Å2
ΔGint-135 kcal/mol
Surface area29960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.978, 42.071, 91.837
Angle α, β, γ (deg.)90.0, 97.0, 90.0
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein 3-Keto-L-Gulonate 6-Phosphate Decarboxylase / E.C.4.1.2.- / hexulose-6-phosphate synthase / HUMPS / D-arabino 3-hexulose 6-phosphate formaldehyde lyase


Mass: 23603.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P39304, Lyases; Carbon-carbon lyases; Aldehyde-lyases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-LG6 / L-GULURONIC ACID 6-PHOSPHATE


Mass: 276.135 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13O10P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7
Details: 18% MePEG 5000, 50 mM bis-Tris propane, pH 7.0, 25 mM L-gulonate 6-phosphate. micro-batch at 298K
Crystal grow
*PLUS
pH: 7.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMHEPES11pH7.5
25 mM11MgCl2
3100 mM11NaCl
415 mg/mlprotein11
518 %MePEG500011
650 mMsodium potassium phosphate11
750 mMbis-Tris-propane11pH7.0

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Data collection

DiffractionMean temperature: 274 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: May 1, 2001 / Details: mirrors
RadiationMonochromator: Gobel mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 35323 / Num. obs: 32215 / % possible obs: 91.2 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.03 / Net I/σ(I): 15.7
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 3.4 / % possible all: 80
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / Num. obs: 22847 / Num. measured all: 56895 / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 77.9 % / Rmerge(I) obs: 0.099

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Processing

Software
NameClassification
CNSrefinement
FRMABOdata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KV8

1kv8


Resolution: 2.2→30 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1053 4.9 %RANDOM
Rwork0.18 ---
all0.18 24293 --
obs0.18 21499 88.5 %-
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3278 0 36 193 3507
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.006
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor obs: 0.18 / Rfactor Rfree: 0.212 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.2

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