[English] 日本語
Yorodumi
- PDB-3ctm: Crystal Structure of a Carbonyl Reductase from Candida Parapsilos... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ctm
TitleCrystal Structure of a Carbonyl Reductase from Candida Parapsilosis with anti-Prelog Stereo-specificity
Components(Carbonyl Reductase) x 2
KeywordsOXIDOREDUCTASE / alcohol dehydrogenase / Candida parapsilosis / short-chain dehydrogenases/reductases (SDR)
Function / homology
Function and homology information


oxidoreductase activity, acting on NAD(P)H, oxygen as acceptor / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / metabolic process
Similarity search - Function
Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCandida parapsilosis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsZhang, R. / Zhu, G. / Li, X. / Xu, Y. / Zhang, X.C. / Rao, Z.
Funding support China, 4items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)20376031 China
National Science Foundation (NSF, China)20776060 China
Ministry of Science and Technology (MoST, China)2003CB716008 China
Ministry of Science and Technology (MoST, China)2007AA02Z200 China
Citation
Journal: Protein Sci. / Year: 2008
Title: Crystal structure of a carbonyl reductase from Candida parapsilosis with anti-Prelog stereospecificity.
Authors: Zhang, R. / Zhu, G. / Zhang, W. / Cao, S. / Ou, X. / Li, X. / Bartlam, M. / Xu, Y. / Zhang, X.C. / Rao, Z.
#1: Journal: EMBO J / Year: 2022
Title: Oligomeric interactions maintain active-site structure in a noncooperative enzyme family.
Authors: Yaohui Li / Rongzhen Zhang / Chi Wang / Farhad Forouhar / Oliver B Clarke / Sergey Vorobiev / Shikha Singh / Gaetano T Montelione / Thomas Szyperski / Yan Xu / John F Hunt /
Abstract: The evolutionary benefit accounting for widespread conservation of oligomeric structures in proteins lacking evidence of intersubunit cooperativity remains unclear. Here, crystal and cryo-EM ...The evolutionary benefit accounting for widespread conservation of oligomeric structures in proteins lacking evidence of intersubunit cooperativity remains unclear. Here, crystal and cryo-EM structures, and enzymological data, demonstrate that a conserved tetramer interface maintains the active-site structure in one such class of proteins, the short-chain dehydrogenase/reductase (SDR) superfamily. Phylogenetic comparisons support a significantly longer polypeptide being required to maintain an equivalent active-site structure in the context of a single subunit. Oligomerization therefore enhances evolutionary fitness by reducing the metabolic cost of enzyme biosynthesis. The large surface area of the structure-stabilizing oligomeric interface yields a synergistic gain in fitness by increasing tolerance to activity-enhancing yet destabilizing mutations. We demonstrate that two paralogous SDR superfamily enzymes with different specificities can form mixed heterotetramers that combine their individual enzymological properties. This suggests that oligomerization can also diversify the functions generated by a given metabolic investment, enhancing the fitness advantage provided by this architectural strategy.
History
DepositionApr 14, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jun 8, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / cell ...atom_site / cell / chem_comp / database_2 / database_PDB_caveat / diffrn / diffrn_detector / diffrn_radiation_wavelength / diffrn_source / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_database_status / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range / symmetry
Item: _cell.Z_PDB / _cell.volume ..._cell.Z_PDB / _cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn.pdbx_serial_crystal_experiment / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _pdbx_contact_author.email / _pdbx_contact_author.fax / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_contact_author.name_first / _pdbx_contact_author.name_salutation / _pdbx_database_status.SG_entry / _pdbx_entity_nonpoly.entity_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_cross_valid_method / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _reflns.B_iso_Wilson_estimate / _struct.pdbx_CASP_flag / _struct_asym.entity_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq.ref_id / _symmetry.space_group_name_Hall
Description: Model completeness / Provider: author / Type: Coordinate replacement
Revision 2.1Jul 27, 2022Group: Database references / Category: citation / citation_author
Revision 2.2Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbonyl Reductase
B: Carbonyl Reductase
D: Carbonyl Reductase
C: Carbonyl Reductase
E: Carbonyl Reductase
F: Carbonyl Reductase
G: Carbonyl Reductase
H: Carbonyl Reductase


Theoretical massNumber of molelcules
Total (without water)250,0448
Polymers250,0448
Non-polymers00
Water6,612367
1
A: Carbonyl Reductase
B: Carbonyl Reductase
D: Carbonyl Reductase
C: Carbonyl Reductase


Theoretical massNumber of molelcules
Total (without water)124,9844
Polymers124,9844
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14110 Å2
ΔGint-120 kcal/mol
Surface area41880 Å2
MethodPISA
2
E: Carbonyl Reductase
F: Carbonyl Reductase
G: Carbonyl Reductase
H: Carbonyl Reductase


Theoretical massNumber of molelcules
Total (without water)125,0604
Polymers125,0604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14880 Å2
ΔGint-122 kcal/mol
Surface area41530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.728, 142.756, 151.838
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

-
Components

#1: Protein
Carbonyl Reductase / S-reductase


Mass: 31265.051 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida parapsilosis (yeast) / Gene: DQ675534 / Plasmid: pETSCR / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: B2KJ46, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Protein Carbonyl Reductase / S-reductase


Mass: 31188.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida parapsilosis (yeast) / Gene: DQ675534 / Plasmid: pETSCR / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: B2KJ46, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: buffer: 18%(w/v) PEG2K MME, 8%(v/v) isopropanol, pH 8.5, droplet: 20mg/ml SCR, 20mM Tris-HCl, 150mM NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Apr 1, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.69→41.67 Å / Num. obs: 65214 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 43.61 Å2 / Rmerge(I) obs: 0.142 / Rsym value: 0.066 / Net I/σ(I): 11.2
Reflection shellResolution: 2.69→2.76 Å / Rmerge(I) obs: 0.142 / Num. unique obs: 65214

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
REFMACpackagephasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H5Q

1h5q


Resolution: 2.69→41.66 Å / SU ML: 0.3733 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.0026
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2677 3213 5.08 %RANDOM
Rwork0.1803 60041 --
obs0.1846 63254 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.45 Å2
Refinement stepCycle: LAST / Resolution: 2.69→41.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16374 0 0 367 16741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008416740
X-RAY DIFFRACTIONf_angle_d0.972922742
X-RAY DIFFRACTIONf_chiral_restr0.06262563
X-RAY DIFFRACTIONf_plane_restr0.00642869
X-RAY DIFFRACTIONf_dihedral_angle_d6.64472261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.730.36831390.24672266X-RAY DIFFRACTION88.52
2.73-2.780.38211600.23752577X-RAY DIFFRACTION100
2.78-2.820.32911320.22812594X-RAY DIFFRACTION99.93
2.82-2.870.35251270.21212613X-RAY DIFFRACTION100
2.87-2.920.31281560.21052588X-RAY DIFFRACTION100
2.92-2.980.31831380.20532604X-RAY DIFFRACTION100
2.98-3.040.30141290.21322575X-RAY DIFFRACTION100
3.04-3.110.30471350.20182625X-RAY DIFFRACTION100
3.11-3.180.3071570.22575X-RAY DIFFRACTION100
3.18-3.260.31441300.19312598X-RAY DIFFRACTION99.96
3.26-3.350.31271350.19542614X-RAY DIFFRACTION100
3.35-3.440.29491310.18622603X-RAY DIFFRACTION100
3.44-3.550.28021290.18432632X-RAY DIFFRACTION100
3.55-3.680.30181380.18582607X-RAY DIFFRACTION100
3.68-3.830.2531410.16772602X-RAY DIFFRACTION99.64
3.83-40.23081600.16872614X-RAY DIFFRACTION99.71
4-4.210.23691350.15992638X-RAY DIFFRACTION99.96
4.21-4.480.23951470.15222625X-RAY DIFFRACTION99.96
4.48-4.820.22821360.14512625X-RAY DIFFRACTION99.86
4.82-5.310.25231360.15892675X-RAY DIFFRACTION100
5.31-6.070.26171540.1732659X-RAY DIFFRACTION100
6.07-7.640.2291320.182717X-RAY DIFFRACTION100
7.65-41.660.2061360.17572815X-RAY DIFFRACTION99.26

+
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://pdbjlvh1.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