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- PDB-4lhc: Crystal structure of Synechocystis sp. PCC 6803 glycine decarboxy... -

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Basic information

Entry
Database: PDB / ID: 4lhc
TitleCrystal structure of Synechocystis sp. PCC 6803 glycine decarboxylase (P-protein), holo form with pyridoxal-5'-phosphate and glycine
ComponentsGlycine dehydrogenase [decarboxylating]
KeywordsOXIDOREDUCTASE / alpha(2) homodimer / dehydrogenase (decarboxylating) / cofactor pyridoxal 5'-phosphate
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
BICARBONATE ION / GLYCINE / PHOSPHATE ION / Glycine dehydrogenase (decarboxylating)
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 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
DepositionJul 1, 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 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)217,58333
Polymers215,2982
Non-polymers2,28431
Water25,1131394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12700 Å2
ΔGint-28 kcal/mol
Surface area58310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.050, 160.050, 159.833
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11B-1771-

HOH

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 107649.172 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)

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Non-polymers , 6 types, 1425 molecules

#2: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1394 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5
Details: 100 mM Bicine pH 9, 1.6 M (NH4)3PO4, 5 mM TCEP and 0.2 mM PLP, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2011 / Details: multilayer mirror
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 1.899→99 Å / Num. all: 185699 / Num. obs: 185454 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.4
Reflection shellResolution: 1.899→1.97 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 4.3 / % possible all: 99.1

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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 4LGL

4lgl


Resolution: 1.899→49.783 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 17.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1856 9313 5.02 %
Rwork0.1546 --
obs0.1562 185406 99.89 %
all-185699 -
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.894 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1334 Å2-0 Å20 Å2
2---1.1334 Å2-0 Å2
3---2.2669 Å2
Refinement stepCycle: LAST / Resolution: 1.899→49.783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14486 0 142 1394 16022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715174
X-RAY DIFFRACTIONf_angle_d1.07620639
X-RAY DIFFRACTIONf_dihedral_angle_d13.9165531
X-RAY DIFFRACTIONf_chiral_restr0.0732290
X-RAY DIFFRACTIONf_plane_restr0.0052702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.899-1.92060.22412970.19745701X-RAY DIFFRACTION98
1.9206-1.94320.24432930.18565888X-RAY DIFFRACTION100
1.9432-1.96690.20873130.17055812X-RAY DIFFRACTION100
1.9669-1.99180.18453070.15995791X-RAY DIFFRACTION100
1.9918-2.0180.19353120.15735869X-RAY DIFFRACTION100
2.018-2.04560.20843100.16295806X-RAY DIFFRACTION100
2.0456-2.07490.20892850.1595872X-RAY DIFFRACTION100
2.0749-2.10580.18833180.15365859X-RAY DIFFRACTION100
2.1058-2.13870.1822920.14645795X-RAY DIFFRACTION100
2.1387-2.17380.18412860.14765838X-RAY DIFFRACTION100
2.1738-2.21130.18883160.14925826X-RAY DIFFRACTION100
2.2113-2.25150.18563190.14915895X-RAY DIFFRACTION100
2.2515-2.29480.20062940.15145792X-RAY DIFFRACTION100
2.2948-2.34160.16773130.1475832X-RAY DIFFRACTION100
2.3416-2.39250.23160.15585879X-RAY DIFFRACTION100
2.3925-2.44820.20273180.15435833X-RAY DIFFRACTION100
2.4482-2.50940.18283050.16095859X-RAY DIFFRACTION100
2.5094-2.57730.20733300.16245855X-RAY DIFFRACTION100
2.5773-2.65310.18673460.16295801X-RAY DIFFRACTION100
2.6531-2.73870.19773090.15645850X-RAY DIFFRACTION100
2.7387-2.83660.21423110.15775904X-RAY DIFFRACTION100
2.8366-2.95020.1923500.1585842X-RAY DIFFRACTION100
2.9502-3.08440.18193160.16745902X-RAY DIFFRACTION100
3.0844-3.2470.21242930.16795870X-RAY DIFFRACTION100
3.247-3.45040.18463070.16195908X-RAY DIFFRACTION100
3.4504-3.71670.17982830.14985981X-RAY DIFFRACTION100
3.7167-4.09060.14583380.13015881X-RAY DIFFRACTION100
4.0906-4.68210.15463160.12595965X-RAY DIFFRACTION100
4.6821-5.89750.17233280.1495998X-RAY DIFFRACTION100
5.8975-49.79980.18162920.17336189X-RAY DIFFRACTION99
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)
10.399-0.04490.02850.3674-0.00980.3106-0.0001-0.00430.0765-0.0157-0.0243-0.05090.01150.02860.02010.0861-0.0089-0.00630.04680.00910.082489.84171.961935.7913
20.27640.0920.00230.44710.00340.2807-0.01520.01120.0357-0.013-0.00320.10260.0067-0.05750.01580.06640.0053-0.01320.0649-0.00670.08348.2709-8.644341.0188
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 15:977)
2X-RAY DIFFRACTION2chain 'B' and (resseq 14:977)

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