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- PDB-4lgl: Crystal Structure of Glycine Decarboxylase P-protein from Synecho... -

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Basic information

Entry
Database: PDB / ID: 4lgl
TitleCrystal Structure of Glycine Decarboxylase P-protein from Synechocystis sp. PCC 6803, apo form
ComponentsGlycine dehydrogenase [decarboxylating]
KeywordsOXIDOREDUCTASE / alpha(2) homodimeric / dehydrogenase (decarboxylating) / S / S-(2-hydroxyethyl)thiocysteine
Function / homology
Function and homology information


glycine dehydrogenase (aminomethyl-transferring) / glycine dehydrogenase (decarboxylating) activity / glycine decarboxylation via glycine cleavage system / glycine cleavage complex / glycine binding / pyridoxal phosphate binding / cytosol
Similarity search - Function
Glycine dehydrogenase (decarboxylating) / Glycine cleavage system P protein / : / : / Glycine cleavage system P-protein / Glycine dehydrogenase, C-terminal domain / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Glycine dehydrogenase (decarboxylating)
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0004 Å
AuthorsHasse, D. / Andersson, E. / Carlsson, G. / Masloboy, A. / Hagemann, M. / Bauwe, H. / Andersson, I.
Citation
Journal: J.Biol.Chem. / Year: 2013
Title: Structure of the Homodimeric Glycine Decarboxylase P-protein from Synechocystis sp. PCC 6803 Suggests a Mechanism for Redox Regulation.
Authors: Hasse, D. / Andersson, E. / Carlsson, G. / Masloboy, A. / Hagemann, M. / Bauwe, H. / Andersson, I.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Crystallization and preliminary X-ray diffraction analyses of the homodimeric glycine decarboxylase (P-protein) from the cyanobacterium Synechocystis sp. PCC 6803.
Authors: Hasse, D. / Hagemann, M. / Andersson, I. / Bauwe, H.
History
DepositionJun 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Dec 25, 2013Group: Database references
Revision 1.3Sep 20, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycine dehydrogenase [decarboxylating]
B: Glycine dehydrogenase [decarboxylating]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,4626
Polymers215,1472
Non-polymers3154
Water15,583865
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-41 kcal/mol
Surface area58490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.299, 135.814, 179.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycine dehydrogenase [decarboxylating] / Glycine cleavage system P-protein / Glycine decarboxylase


Mass: 107573.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Kazusa / Gene: gcvP, slr0293 / Plasmid: pBAD-slr0293 / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194
References: UniProt: P74416, glycine dehydrogenase (aminomethyl-transferring)
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 865 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 100 mM Tris-HCl pH 7.75, 17% PEG 3350, 0.25 M LiCl and 10 mM 2-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2008
RadiationMonochromator: na / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→54.11 Å / Num. all: 158584 / Num. obs: 158314 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 26.88
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 3.53 / Num. unique all: 15696 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WYT heterodimer

1wyt


Resolution: 2.0004→54.107 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 7941 5.02 %random
Rwork0.1606 ---
all0.1594 158584 --
obs0.1622 158203 99.81 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.935 Å2 / ksol: 0.338 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.2523 Å2-0 Å2-0 Å2
2---4.4343 Å20 Å2
3----4.818 Å2
Refinement stepCycle: LAST / Resolution: 2.0004→54.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14441 0 18 865 15324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714966
X-RAY DIFFRACTIONf_angle_d1.05820361
X-RAY DIFFRACTIONf_dihedral_angle_d13.3295467
X-RAY DIFFRACTIONf_chiral_restr0.0752260
X-RAY DIFFRACTIONf_plane_restr0.0052670
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0004-2.02310.30542580.22234929X-RAY DIFFRACTION99
2.0231-2.04690.22832610.20214958X-RAY DIFFRACTION100
2.0469-2.07190.2462680.18464976X-RAY DIFFRACTION100
2.0719-2.09810.222520.18124965X-RAY DIFFRACTION100
2.0981-2.12570.20842510.17174990X-RAY DIFFRACTION100
2.1257-2.15480.23482490.16864972X-RAY DIFFRACTION100
2.1548-2.18560.22292590.17184998X-RAY DIFFRACTION100
2.1856-2.21820.19062590.16064958X-RAY DIFFRACTION100
2.2182-2.25290.19722620.15674975X-RAY DIFFRACTION100
2.2529-2.28980.1892800.16194966X-RAY DIFFRACTION100
2.2898-2.32930.19392650.15884964X-RAY DIFFRACTION100
2.3293-2.37170.20862630.15584985X-RAY DIFFRACTION100
2.3717-2.41730.23962720.16774990X-RAY DIFFRACTION100
2.4173-2.46660.20992820.16764964X-RAY DIFFRACTION100
2.4666-2.52030.20822610.16995009X-RAY DIFFRACTION100
2.5203-2.57890.22242690.16894964X-RAY DIFFRACTION100
2.5789-2.64340.21612660.17695018X-RAY DIFFRACTION100
2.6434-2.71490.21882830.17514994X-RAY DIFFRACTION100
2.7149-2.79470.2272560.1674975X-RAY DIFFRACTION100
2.7947-2.88490.19182760.1645014X-RAY DIFFRACTION100
2.8849-2.9880.19292680.16985019X-RAY DIFFRACTION100
2.988-3.10770.212590.17675035X-RAY DIFFRACTION100
3.1077-3.24910.20712880.18144989X-RAY DIFFRACTION100
3.2491-3.42040.2192430.1745048X-RAY DIFFRACTION100
3.4204-3.63460.17822570.1675065X-RAY DIFFRACTION100
3.6346-3.91520.15742480.14955055X-RAY DIFFRACTION100
3.9152-4.3090.16412970.1365035X-RAY DIFFRACTION99
4.309-4.93220.16072650.12895034X-RAY DIFFRACTION99
4.9322-6.21260.17232620.1525148X-RAY DIFFRACTION100
6.2126-54.12650.17452620.15625270X-RAY DIFFRACTION98
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)
10.6318-0.1561-0.21250.6787-0.11250.7635-0.00080.0315-0.0026-0.1054-0.0751-0.08790.06710.19680.0630.16680.0337-0.00280.20770.01860.1379-13.1647-17.967119.8353
20.6824-0.1262-0.14230.64970.16880.938-0.0393-0.11740.25970.0130.0086-0.0473-0.278-0.02160.01380.22060.0426-0.05630.135-0.07140.2532-34.59811.450244.3764
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resseq 18:975)
2X-RAY DIFFRACTION2chain 'A' and (resseq 20:978)

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