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- PDB-1q6r: Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bou... -

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Basic information

Entry
Database: PDB / ID: 1q6r
TitleStructure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L-xylulose 5-phosphate
Components3-keto-L-gulonate 6-phosphate decarboxylase
KeywordsLYASE / BETA 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-XYLULOSE 5-PHOSPHATE / 3-keto-L-gulonate-6-phosphate decarboxylase UlaD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsWise, E.L. / Yew, W.S. / Gerlt, J.A. / Rayment, I.
CitationJournal: Biochemistry / Year: 2003
Title: Structural Evidence for a 1,2-Enediolate Intermediate in the Reaction Catalyzed by 3-Keto-l-Gulonate 6-Phosphate Decarboxylase, a Member of the Orotidine 5'-Monophosphate Decarboxylase Suprafamily
Authors: Wise, E.L. / Yew, W.S. / Gerlt, J.A. / Rayment, I.
History
DepositionAug 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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)47,6876
Polymers47,2062
Non-polymers4814
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-34 kcal/mol
Surface area16190 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)95,37412
Polymers94,4124
Non-polymers9628
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area10720 Å2
ΔGint-74 kcal/mol
Surface area30050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.912, 41.580, 91.627
Angle α, β, γ (deg.)90.00, 96.41, 90.00
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.- / Probable 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) / Production host: Escherichia coli (E. coli)
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-LX1 / L-XYLULOSE 5-PHOSPHATE


Mass: 216.126 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H13O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.13 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7
Details: 16% MePEG 2000, 50 mM BTP pH 7.0, 5 mM MgCl2, microbatch, temperature 298K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMHEPES11pH7.5
25 mM11MgCl2
3100 mM11NaCl
415 mg/mlprotein11
5100 mMBTP11pH7.0
65 mM11MgCl2
716 %PEG5000 ME11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.987 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 5, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.76→100 Å / Num. obs: 45531 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Net I/σ(I): 18.1
Reflection shellResolution: 1.76→1.82 Å / Mean I/σ(I) obs: 2.62 / % possible all: 98.1
Reflection
*PLUS
Num. obs: 46548 / Num. measured all: 653244 / Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 98.1 % / Rmerge(I) obs: 0.482

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
SCALEPACKdata scaling
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→91.29 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.334 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22875 2276 5 %RANDOM
Rwork0.18954 ---
obs0.1915 43255 97.97 %-
all-45531 --
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: 26.359 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å20.53 Å2
2--1.51 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.76→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3267 0 28 303 3598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0213348
X-RAY DIFFRACTIONr_bond_other_d0.0020.023131
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.9444548
X-RAY DIFFRACTIONr_angle_other_deg1.68537226
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2035426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1010.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023740
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02672
X-RAY DIFFRACTIONr_nbd_refined0.2330.2679
X-RAY DIFFRACTIONr_nbd_other0.2480.23552
X-RAY DIFFRACTIONr_nbtor_other0.0830.22060
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2224
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0861.52119
X-RAY DIFFRACTIONr_mcangle_it1.97323381
X-RAY DIFFRACTIONr_scbond_it3.05931229
X-RAY DIFFRACTIONr_scangle_it4.954.51167
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.268 176
Rwork0.234 3187
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection obs: 45980 / Num. reflection Rfree: 2482 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.72

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