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

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Basic information

Entry
Database: PDB / ID: 4lhd
TitleCrystal structure of Synechocystis sp. PCC 6803 glycine decarboxylase (P-protein), holo form with pyridoxal-5'-phosphate and glycine, closed flexible loop
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: 1.7959 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)217,18029
Polymers215,2982
Non-polymers1,88127
Water24,7171372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11640 Å2
ΔGint-22 kcal/mol
Surface area57520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.992, 159.992, 159.680
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-1773-

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 , 5 types, 1399 molecules

#2: Chemical
ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical
ChemComp-BCT / BICARBONATE ION


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


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1372 / 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: 55.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM Bicine pH 9, 1.6 M (NH4)3PO4, 5 mM TCEP and 0.2 mM PLP, VAPOR DIFFUSION, HANGING DROP, 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: 1.7959→99 Å / Num. all: 218802 / Num. obs: 217331 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 16.6
Reflection shellResolution: 1.7959→1.86 Å / Redundancy: 4 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 3.3 / % possible all: 95.4

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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 4LHC

4lhc


Resolution: 1.7959→49.762 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 17.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1914 10958 5.04 %
Rwork0.1625 --
obs0.1639 217318 99.35 %
all-218802 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.999 Å2 / ksol: 0.38 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3515 Å2-0 Å20 Å2
2---0.3515 Å2-0 Å2
3---0.7029 Å2
Refinement stepCycle: LAST / Resolution: 1.7959→49.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14557 0 118 1372 16047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715167
X-RAY DIFFRACTIONf_angle_d1.09720624
X-RAY DIFFRACTIONf_dihedral_angle_d13.6235541
X-RAY DIFFRACTIONf_chiral_restr0.0762303
X-RAY DIFFRACTIONf_plane_restr0.0052691
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7959-1.81630.29583370.23766054X-RAY DIFFRACTION88
1.8163-1.83760.26713720.21996824X-RAY DIFFRACTION99
1.8376-1.860.22883920.20156770X-RAY DIFFRACTION99
1.86-1.88360.23423420.19516819X-RAY DIFFRACTION99
1.8836-1.90840.21653630.18666814X-RAY DIFFRACTION99
1.9084-1.93450.22733920.17956850X-RAY DIFFRACTION100
1.9345-1.96220.19813720.16556860X-RAY DIFFRACTION100
1.9622-1.99150.20083810.15956805X-RAY DIFFRACTION100
1.9915-2.02260.20873750.15976945X-RAY DIFFRACTION100
2.0226-2.05570.18653510.16116897X-RAY DIFFRACTION100
2.0557-2.09120.19933860.15876807X-RAY DIFFRACTION100
2.0912-2.12920.20623540.15646919X-RAY DIFFRACTION100
2.1292-2.17020.19343690.15666837X-RAY DIFFRACTION100
2.1702-2.21450.20813750.15866904X-RAY DIFFRACTION100
2.2145-2.26260.19143440.15736913X-RAY DIFFRACTION100
2.2626-2.31520.20743590.15986902X-RAY DIFFRACTION100
2.3152-2.37310.21013520.15616888X-RAY DIFFRACTION100
2.3731-2.43730.20093700.15916889X-RAY DIFFRACTION100
2.4373-2.5090.19183650.16666915X-RAY DIFFRACTION100
2.509-2.590.213850.1676876X-RAY DIFFRACTION100
2.59-2.68260.20013740.16876915X-RAY DIFFRACTION100
2.6826-2.790.18613730.16066925X-RAY DIFFRACTION100
2.79-2.91690.19543280.16196966X-RAY DIFFRACTION100
2.9169-3.07070.19213960.17016890X-RAY DIFFRACTION100
3.0707-3.2630.19473500.176990X-RAY DIFFRACTION100
3.263-3.51490.19693610.16536935X-RAY DIFFRACTION100
3.5149-3.86850.16173640.1476967X-RAY DIFFRACTION100
3.8685-4.4280.14963600.13247028X-RAY DIFFRACTION100
4.428-5.57760.16353610.14797036X-RAY DIFFRACTION100
5.5776-49.78090.16823550.17567220X-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)
10.3862-0.042-0.01180.30510.02960.2824-0.0112-0.0232-0.0952-0.0083-0.01490.03950.02580.0190.01980.0509-0.02280.01620.05680.00150.07543.1153-78.927444.1713
20.30320.1356-0.00890.3532-0.00710.25-0.0068-0.00280.08340.0149-0.00880.0888-0.0577-0.02950.01190.04060.0018-0.00230.0541-0.01570.066731.6218-37.394138.8874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 15:977)
2X-RAY DIFFRACTION2chain 'B' and (resseq 15:977)

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