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- PDB-1so3: Crystal structure of H136A mutant of 3-keto-L-gulonate 6-phosphat... -

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Basic information

Entry
Database: PDB / ID: 1so3
TitleCrystal structure of H136A mutant of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L-threonohydroxamate 4-phosphate
Components3-keto-L-gulonate 6-phosphate decarboxylase
KeywordsLYASE / TIM Barrel / 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-THREONOHYDROXAMATE 4-PHOSPHATE / 3-keto-L-gulonate-6-phosphate decarboxylase UlaD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWise, E.L. / Yew, W.S. / Gerlt, J.A. / Rayment, I.
CitationJournal: Biochemistry / Year: 2004
Title: Evolution of Enzymatic Activities in the Orotidine 5'-Monophosphate Decarboxylase Suprafamily: Crystallographic Evidence for a Proton Relay System in the Active Site of 3-Keto-l-gulonate 6- ...Title: Evolution of Enzymatic Activities in the Orotidine 5'-Monophosphate Decarboxylase Suprafamily: Crystallographic Evidence for a Proton Relay System in the Active Site of 3-Keto-l-gulonate 6-Phosphate Decarboxylase(,)
Authors: Wise, E.L. / Yew, W.S. / Gerlt, J.A. / Rayment, I.
History
DepositionMar 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)47,5876
Polymers47,0722
Non-polymers5154
Water9,044502
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-40 kcal/mol
Surface area16050 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)95,17412
Polymers94,1444
Non-polymers1,0308
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area11290 Å2
ΔGint-87 kcal/mol
Surface area29720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.116, 42.059, 91.070
Angle α, β, γ (deg.)90.00, 97.06, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2338-

HOH

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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: 23535.971 Da / Num. of mol.: 2 / Mutation: His136Ala
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: UlaD / 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-TX4 / L-THREONOHYDROXAMATE 4-PHOSPHATE


Mass: 233.114 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.18 Å3/Da / Density % sol: 43.2 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7
Details: 16% PEG 5000, methyl ether, 100 mM BTP pH 7.0, 5 mM MgCl2, Microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→91.29 Å / Num. all: 36727 / Num. obs: 36727 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.065 / Net I/σ(I): 26
Reflection shellResolution: 1.9→1.97 Å / % possible all: 91.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.24refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→91.29 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.707 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19247 1839 5 %RANDOM
Rwork0.14792 ---
all0.1501 36727 --
obs0.1501 34888 99.29 %-
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: 19.972 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å20.29 Å2
2--1.45 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 30 502 3829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213379
X-RAY DIFFRACTIONr_bond_other_d0.0020.023159
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.9494583
X-RAY DIFFRACTIONr_angle_other_deg1.93337302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9195425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1060.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023757
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02679
X-RAY DIFFRACTIONr_nbd_refined0.2360.2747
X-RAY DIFFRACTIONr_nbd_other0.2470.23723
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.21955
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2353
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0110.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7731.52125
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34623396
X-RAY DIFFRACTIONr_scbond_it2.2631254
X-RAY DIFFRACTIONr_scangle_it3.6324.51187
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.948 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.328 125
Rwork0.285 2304

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