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Basic information

Entry
Database: PDB / ID: 3zgb
TitleGreater efficiency of photosynthetic carbon fixation due to single amino acid substitution
ComponentsPHOSPHOENOLPYRUVATE CARBOXYLASE
KeywordsLYASE
Function / homology
Function and homology information


phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / leaf development / apoplast / carbon fixation / tricarboxylic acid cycle / photosynthesis / chloroplast / cytosol
Similarity search - Function
Phosphoenolpyruvate carboxylase, Lys active site / Phosphoenolpyruvate carboxylase / Phosphoenolpyruvate carboxylase, bacterial/plant-type / Phosphoenolpyruvate carboxylase, His active site / Phosphoenolpyruvate carboxylase / Phosphoenolpyruvate carboxylase active site 2. / Phosphoenolpyruvate carboxylase active site 1. / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
ASPARTIC ACID / Phosphoenolpyruvate carboxylase
Similarity search - Component
Biological speciesFlaveria pringlei (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsPaulus, J.K. / Schlieper, D. / Groth, G.
CitationJournal: Nat.Commun. / Year: 2013
Title: Greater Efficiency of Photosynthetic Carbon Fixation due to Single Amino Acid Substitution
Authors: Paulus, J.K. / Schlieper, D. / Groth, G.
History
DepositionDec 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2Dec 3, 2014Group: Data collection / Non-polymer description / Structure summary
Revision 1.3Dec 17, 2014Group: Data collection
Revision 1.4Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOENOLPYRUVATE CARBOXYLASE
B: PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,71910
Polymers222,9452
Non-polymers7758
Water1,00956
1
A: PHOSPHOENOLPYRUVATE CARBOXYLASE
B: PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules

A: PHOSPHOENOLPYRUVATE CARBOXYLASE
B: PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)447,43920
Polymers445,8894
Non-polymers1,54916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area14460 Å2
ΔGint-114.2 kcal/mol
Surface area134490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.549, 121.700, 132.031
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PHOSPHOENOLPYRUVATE CARBOXYLASE / PEPC / PEPCASE / PPCA


Mass: 111472.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE GENE NAME OF THE PROTEIN IS PPCA / Source: (gene. exp.) Flaveria pringlei (plant) / Plasmid: PETEV16B / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD
References: UniProt: Q01647, phosphoenolpyruvate carboxylase
#2: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CRYSTALLIZED SEQUENCE ACTUALLY MAPS TO NCBI ACCESSION CODE Z48966 WITHOUT ANY CONFLICTS OR GAPS. ...THE CRYSTALLIZED SEQUENCE ACTUALLY MAPS TO NCBI ACCESSION CODE Z48966 WITHOUT ANY CONFLICTS OR GAPS. THE CLOSEST UNIPROT MATCH FOR THE SEQUENCE IS Q01647

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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: 3.2 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growpH: 5.6
Details: 0.2 M AMMONIUM SULFATE, 0.1 M TRI-SODIUM CITRATE/HCL PH 5.6, 10 % (W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.12678
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12678 Å / Relative weight: 1
ReflectionResolution: 2.71→165.55 Å / Num. obs: 71548 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 15.8 % / Biso Wilson estimate: 55.8 Å2 / Rsym value: 0.099 / Net I/σ(I): 6.3
Reflection shellResolution: 2.71→2.86 Å / Redundancy: 16.4 % / Mean I/σ(I) obs: 2 / Rsym value: 0.334 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZBE

3zbe


Resolution: 2.71→78.72 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.918 / SU B: 21.152 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.567 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22985 1486 2 %RANDOM
Rwork0.18769 ---
obs0.18854 71548 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2--0.14 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.71→78.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14750 0 46 56 14852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01915093
X-RAY DIFFRACTIONr_bond_other_d0.0040.0210545
X-RAY DIFFRACTIONr_angle_refined_deg1.7581.97320405
X-RAY DIFFRACTIONr_angle_other_deg1.175325584
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9251826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00523.598731
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.579152710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5415134
X-RAY DIFFRACTIONr_chiral_restr0.0940.22250
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02116632
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023106
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.71→2.78 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 100 -
Rwork0.226 4897 -
obs--100 %
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)
10.79790.11030.05141.56240.04020.8391-0.11640.09250.1846-0.29750.0794-0.16620.05970.03220.0370.50620.0415-0.01820.03680.02080.134912.39845.343.844
20.4103-0.13810.00271.7494-0.74320.67560.0305-0.05590.09460.15390.05810.1454-0.0156-0.0925-0.08860.5094-0.0054-0.00570.039-0.03560.1306-6.55333.77526.828
31.57710.28810.1191.3133-0.17851.0003-0.04490.0777-0.1102-0.2448-0.0146-0.31790.29010.20670.05950.5720.09070.03120.0687-0.02620.15718.75722.4987.06
41.48670.1816-0.13411.64590.01830.8893-0.06490.04520.32290.30050.06270.06580.0522-0.05020.00220.4775-0.10960.0160.04680.00280.1238-16.25450.131-28.959
50.77270.33870.03461.17950.48050.9242-0.05540.1631-0.071-0.17640.0916-0.22110.07430.0254-0.03620.5141-0.09890.09160.1284-0.05460.1458-2.833.181-51.83
61.8034-0.2492-0.07311.96440.1431.1279-0.06660.0541-0.06490.07820.04180.38060.1559-0.26910.02480.4531-0.17680.06120.1812-0.00970.1541-30.17330.689-31.357
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 223
2X-RAY DIFFRACTION2A224 - 704
3X-RAY DIFFRACTION3A705 - 966
4X-RAY DIFFRACTION4B8 - 223
5X-RAY DIFFRACTION5B224 - 704
6X-RAY DIFFRACTION6B705 - 966

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