[English] 日本語
Yorodumi
- PDB-3zge: Greater efficiency of photosynthetic carbon fixation due to singl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zge
TitleGreater efficiency of photosynthetic carbon fixation due to single amino acid substitution
ComponentsC4 PHOSPHOENOLPYRUVATE CARBOXYLASE
KeywordsLYASE / C4 PHOTOSYNTHETIC PATHWAY / CARBON FIXATION / PEP CARBOXYLASE
Function / homology
Function and homology information


C4 photosynthesis / phosphoenolpyruvate carboxylase / phosphoenolpyruvate carboxylase activity / leaf development / apoplast / carbon fixation / tricarboxylic acid cycle / 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 / C4 phosphoenolpyruvate carboxylase
Similarity search - Component
Biological speciesFLAVERIA TRINERVIA (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
B: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,5568
Polymers226,9732
Non-polymers5826
Water3,567198
1
A: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
B: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules

A: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
B: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)455,11116
Polymers453,9464
Non-polymers1,16512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area16500 Å2
ΔGint19 kcal/mol
Surface area167740 Å2
MethodPISA
2
B: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules

B: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,5568
Polymers226,9732
Non-polymers5826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6530 Å2
ΔGint-25.6 kcal/mol
Surface area68470 Å2
MethodPISA
3
A: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules

A: C4 PHOSPHOENOLPYRUVATE CARBOXYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,5568
Polymers226,9732
Non-polymers5826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6390 Å2
ΔGint-24.9 kcal/mol
Surface area69190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.520, 122.110, 131.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein C4 PHOSPHOENOLPYRUVATE CARBOXYLASE / C4 PEPC / C4 PEPCASE / PPCA / PHOTOSYNTHETIC PEPCASE


Mass: 113486.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FLAVERIA TRINERVIA (plant) / Plasmid: PETEV16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P30694, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 5.6
Details: 0.2 M AMMONIUM SULFATE, 0.1 M TRI-SODIUM CITRATE/HCL PH 5.6, 15 % PEG 4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9763
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 11, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.49→37.83 Å / Num. obs: 90203 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 26.2 % / Biso Wilson estimate: 45.2 Å2 / Rsym value: 0.097 / Net I/σ(I): 5.9
Reflection shellResolution: 2.49→2.62 Å / Redundancy: 24 % / Mean I/σ(I) obs: 5.9 / Rsym value: 0.389 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JQO

1jqo


Resolution: 2.49→37 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.918 / SU B: 13.145 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.358 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23719 1845 2 %RANDOM
Rwork0.20358 ---
obs0.20425 90203 99.63 %-
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: 39.521 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.49→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14710 0 36 198 14944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01915045
X-RAY DIFFRACTIONr_bond_other_d0.0050.0210500
X-RAY DIFFRACTIONr_angle_refined_deg1.7941.97220334
X-RAY DIFFRACTIONr_angle_other_deg1.204325494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90251815
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3723.717729
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.89152710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.03915127
X-RAY DIFFRACTIONr_chiral_restr0.0980.22241
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02116551
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023080
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: 2.49→2.554 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 112 -
Rwork0.241 6235 -
obs--99.98 %
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)
11.5302-0.51530.051.6533-0.01860.6156-0.0928-0.1094-0.28240.22230.1015-0.13340.02870.121-0.00870.1047-0.07450.0110.2066-0.00910.150397.650310.8188102.5361
20.49940.07810.02811.193-0.60960.9885-0.00770.1074-0.0701-0.24120.01310.13840.0436-0.0356-0.00540.1038-0.0468-0.05460.15260.02260.066883.712827.286379.3709
32.0955-0.3623-0.00812.1835-0.0831.1589-0.07070.05580.00870.0197-0.031-0.2967-0.17560.22580.10170.1058-0.1444-0.03950.22680.03040.0775111.088430.6068100.9383
41.59140.46220.02931.08180.01690.589-0.07490.2244-0.1561-0.12090.05460.19390.0043-0.12620.02030.08940.04290.04070.1081-0.00190.14369.034715.9442135.3563
50.32190.00510.18191.45170.62450.66980.0356-0.0592-0.1490.25520.0376-0.1010.09550.0034-0.07330.0726-0.0044-0.02020.04330.0330.102588.226626.719158.2517
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more