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- PDB-3fkd: The crystal structure of L-threonine-O-3-phosphate decarboxylase ... -

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Basic information

Entry
Database: PDB / ID: 3fkd
TitleThe crystal structure of L-threonine-O-3-phosphate decarboxylase from Porphyromonas gingivalis
ComponentsL-threonine-O-3-phosphate decarboxylase
KeywordsLYASE / 11247b / structural genomic / L-threonine-O-3-phosphate decarboxylase Porphyromonas gingivalis / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


biosynthetic process / catalytic activity / pyridoxal phosphate binding
Similarity search - Function
Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex ...Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-threonine-O-3-phosphate decarboxylase, putative
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsZhang, Z. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of L-threonine-O-3-phosphate decarboxylase from Porphyromonas gingivalis
Authors: Zhang, Z. / Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionDec 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 13, 2019Group: Derived calculations / Structure summary / Category: struct_conn / struct_keywords
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_keywords.text
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-threonine-O-3-phosphate decarboxylase
B: L-threonine-O-3-phosphate decarboxylase
C: L-threonine-O-3-phosphate decarboxylase
D: L-threonine-O-3-phosphate decarboxylase


Theoretical massNumber of molelcules
Total (without water)161,8344
Polymers161,8344
Non-polymers00
Water5,368298
1
A: L-threonine-O-3-phosphate decarboxylase
D: L-threonine-O-3-phosphate decarboxylase


Theoretical massNumber of molelcules
Total (without water)80,9172
Polymers80,9172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-20 kcal/mol
Surface area27250 Å2
MethodPISA
2
B: L-threonine-O-3-phosphate decarboxylase
C: L-threonine-O-3-phosphate decarboxylase


Theoretical massNumber of molelcules
Total (without water)80,9172
Polymers80,9172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-20 kcal/mol
Surface area26870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.443, 101.513, 93.714
Angle α, β, γ (deg.)90.00, 90.22, 90.00
Int Tables number4
Space group name H-MP1211
Detailsdimer

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Components

#1: Protein
L-threonine-O-3-phosphate decarboxylase


Mass: 40458.566 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: ATCC BAA-308 / W83 / Gene: PG_0012 / Plasmid: BC-pSGX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7MXY2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Sodium citrate tribacic dihydrate pH 5.6, 20% v/v 2-Propanol, 20% PEG 4000, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2008 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 56150 / Num. obs: 56150 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 12.4
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 3.9 / Num. unique all: 7466 / Rsym value: 0.313 / % possible all: 99

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXmodel building
SHARPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→46.857 Å / SU ML: 0.42 / Isotropic thermal model: Isotropic / σ(F): 0.04 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2745 2847 5.07 %RANDOM
Rwork0.224 ---
all0.2492 56150 --
obs0.2266 56150 98.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.394 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1--12.8192 Å217.7907 Å2-4.9715 Å2
2--0 Å2-1.661 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10312 0 0 298 10610
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.028
X-RAY DIFFRACTIONf_angle_deg0.014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54310.30211320.23042581X-RAY DIFFRACTION96
2.5431-2.58940.33981520.24182589X-RAY DIFFRACTION96
2.5894-2.63920.34291370.25582599X-RAY DIFFRACTION98
2.6392-2.69310.3531350.24772617X-RAY DIFFRACTION97
2.6931-2.75160.29841560.23012635X-RAY DIFFRACTION98
2.7516-2.81560.29621290.23292652X-RAY DIFFRACTION98
2.8156-2.8860.31211500.22412630X-RAY DIFFRACTION99
2.886-2.9640.25991290.22272686X-RAY DIFFRACTION99
2.964-3.05120.27841220.22372677X-RAY DIFFRACTION99
3.0512-3.14970.28391370.23192692X-RAY DIFFRACTION99
3.1497-3.26220.26831380.22542664X-RAY DIFFRACTION100
3.2622-3.39280.27771530.2142667X-RAY DIFFRACTION100
3.3928-3.54720.24671490.21282703X-RAY DIFFRACTION100
3.5472-3.73410.25651620.21552664X-RAY DIFFRACTION100
3.7341-3.9680.27891380.20672689X-RAY DIFFRACTION100
3.968-4.27410.22961390.20112708X-RAY DIFFRACTION100
4.2741-4.70390.25361350.19022692X-RAY DIFFRACTION100
4.7039-5.38370.24551550.20262691X-RAY DIFFRACTION100
5.3837-6.77960.29071470.22962728X-RAY DIFFRACTION100
6.7796-46.86480.22471520.22222739X-RAY DIFFRACTION99

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