[English] 日本語
Yorodumi
- PDB-2v8g: Crystal structure of beta-alanine synthase from Saccharomyces klu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2v8g
TitleCrystal structure of beta-alanine synthase from Saccharomyces kluyveri in complex with the product beta-alanine
ComponentsBETA-ALANINE SYNTHASEBeta-ureidopropionase
KeywordsHYDROLASE / DI-ZINC CENTER / AMIDOHYDROLASE / ALPHA AND BETA PROTEIN
Function / homology
Function and homology information


beta-ureidopropionase / beta-ureidopropionase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / metal ion binding
Similarity search - Function
Amidase, carbamoylase-type / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits ...Amidase, carbamoylase-type / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-ALANINE / Beta-alanine synthase
Similarity search - Component
Biological speciesSACCHAROMYCES KLUYVERI (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLundgren, S. / Andersen, B. / Piskur, J. / Dobritzsch, D.
Citation
Journal: J.Biol.Chem. / Year: 2007
Title: Crystal Structures of Yeast -Alanine Synthase Complexes Reveal the Mode of Substrate Binding and Large Scale Domain Closure Movements.
Authors: Lundgren, S. / Andersen, B. / Piskur, J. / Dobritzsch, D.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Yeast Beta-Alanine Synthase Shares a Structural Scaffold and Origin with Dizinc-Dependent Exopeptidases
Authors: Lundgren, S. / Gojkovic, Z. / Piskur, J. / Dobritzsch, D.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and Preliminary X-Ray Analysis of Beta-Alanine Synthase from the Yeast Saccharomyces Kluyveri
Authors: Dobritzsch, D. / Gojkovic, Z. / Andersen, B. / Piskur, J.
History
DepositionAug 7, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA-ALANINE SYNTHASE
B: BETA-ALANINE SYNTHASE
C: BETA-ALANINE SYNTHASE
D: BETA-ALANINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,38118
Polymers208,0274
Non-polymers1,35414
Water3,783210
1
A: BETA-ALANINE SYNTHASE
B: BETA-ALANINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6919
Polymers104,0142
Non-polymers6777
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-41.6 kcal/mol
Surface area39200 Å2
MethodPISA
2
C: BETA-ALANINE SYNTHASE
D: BETA-ALANINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,6919
Polymers104,0142
Non-polymers6777
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-47.6 kcal/mol
Surface area39330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.100, 217.300, 81.600
Angle α, β, γ (deg.)90.00, 91.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUTRPTRPAA28 - 5227 - 51
21LEULEUTRPTRPBB28 - 5227 - 51
31LEULEUTRPTRPCC28 - 5227 - 51
41LEULEUTRPTRPDD28 - 5227 - 51
12HISHISVALVALAA57 - 18956 - 188
22HISHISVALVALBB57 - 18956 - 188
32HISHISVALVALCC57 - 18956 - 188
42HISHISVALVALDD57 - 18956 - 188
13SERSERPHEPHEAA196 - 457195 - 456
23SERSERPHEPHEBB196 - 457195 - 456
33SERSERPHEPHECC196 - 457195 - 456
43SERSERPHEPHEDD196 - 457195 - 456

NCS oper:
IDCodeMatrixVector
1given(-0.675, 0.01, 0.738), (-0.011, -1, 0.003), (0.738, -0.006, 0.675)0.53303, -0.79134, -0.37919
2given(-0.812, 0.003, -0.583), (0.001, -1, -0.006), (-0.583, -0.006, 0.812)66.76126, 74.10693, 21.76338

-
Components

#1: Protein
BETA-ALANINE SYNTHASE / Beta-ureidopropionase


Mass: 52006.809 Da / Num. of mol.: 4 / Fragment: RESIDUES 2-455
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES KLUYVERI (fungus) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96W94, beta-ureidopropionase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BAL / BETA-ALANINE / Β-Alanine


Type: peptide-like / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical
ChemComp-BCN / BICINE / Bicine


Mass: 163.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE N-TERMINAL METHIONINE IS ABSENT, MOST LIKELY DUE TO POSTTRANSLATIONAL MODIFICATION. THE LAST 20 ...THE N-TERMINAL METHIONINE IS ABSENT, MOST LIKELY DUE TO POSTTRANSLATIONAL MODIFICATION. THE LAST 20 AMINO ACIDS CORRESPOND TO THE C-TERMINAL HIS-TAG.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 8.75 / Details: PEG 6000, TRIS PH 8.5, BICINE PH 9.0, LICL.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 59732 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.4
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.29 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R43

1r43


Resolution: 2.5→19.84 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.902 / SU B: 19.409 / SU ML: 0.21 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.242 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2931 4.9 %RANDOM
Rwork0.189 ---
obs0.191 56799 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.36 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å2-1.19 Å2
2---1.64 Å20 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13396 0 64 210 13670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02213781
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1741.94218671
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.56751728
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34324.523650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.108152227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8491568
X-RAY DIFFRACTIONr_chiral_restr0.0850.22006
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210628
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.25787
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.29340
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2443
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3431.58786
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.59213752
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.08635686
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7614.54919
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1672tight positional0.040.05
2B1672tight positional0.030.05
3C1672tight positional0.030.05
4D1672tight positional0.040.05
1A1572medium positional0.350.5
2B1572medium positional0.320.5
3C1572medium positional0.350.5
4D1572medium positional0.370.5
1A1672tight thermal0.070.5
2B1672tight thermal0.060.5
3C1672tight thermal0.050.5
4D1672tight thermal0.060.5
1A1572medium thermal0.492
2B1572medium thermal0.422
3C1572medium thermal0.392
4D1572medium thermal0.452
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.276 202
Rwork0.214 4113
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)
11.2041-0.48810.10281.5369-0.2141.1012-0.01110.05250.01530.01540.0012-0.0495-0.07080.06570.0099-0.1427-0.02240.0088-0.09-0.013-0.15097.946631.17194.8244
20.3177-0.12380.14635.7723-0.54810.10950.0538-0.04860.0208-0.1869-0.09050.27680.1299-0.02480.0366-0.1337-0.0089-0.0015-0.0577-0.0093-0.1646-10.40864.2245-5.6511
30.9899-0.5731-0.2223.00180.51430.9883-0.012-0.14790.0380.1920.0711-0.24350.00950.0261-0.0591-0.0172-0.0004-0.0086-0.0470.0157-0.0286-1.5106-31.94739.0927
40.44481.0164-0.25517.92470.09390.228-0.00070.0905-0.0331-0.4528-0.0349-0.24820.06380.04930.0357-0.08850.02320.0351-0.0614-0.029-0.11943.3767-5.077-11.6357
51.13010.83510.24483.723-0.01851.16180.0020.1967-0.0551-0.21870.027-0.13850.0928-0.0109-0.0290.00180.0031-0.0255-0.03470.0244-0.022820.154868.393931.7401
60.1728-0.62330.16387.1651-0.15790.1932-0.1045-0.01230.05370.6271-0.0419-0.2417-0.16160.11280.14640.0125-0.0218-0.0638-0.0590.0187-0.061727.892941.821152.024
70.90870.41950.02961.5719-0.20791.1806-0.01070.00840.00530.0758-0.0273-0.05630.12680.0780.038-0.11090.02990.0202-0.0580.0075-0.11531.95825.584135.3191
80.3774-0.48340.11986.9424-1.05640.3754-0.0531-0.0021-0.04960.27460.04290.321-0.1532-0.07990.0102-0.07960.00730.0251-0.0569-0.0255-0.131113.888932.015247.5029
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 246
2X-RAY DIFFRACTION1A365 - 458
3X-RAY DIFFRACTION1A500 - 601
4X-RAY DIFFRACTION2A247 - 364
5X-RAY DIFFRACTION3B28 - 246
6X-RAY DIFFRACTION3B365 - 458
7X-RAY DIFFRACTION3B500 - 601
8X-RAY DIFFRACTION4B247 - 364
9X-RAY DIFFRACTION5C27 - 246
10X-RAY DIFFRACTION5C365 - 458
11X-RAY DIFFRACTION5C500 - 601
12X-RAY DIFFRACTION6C247 - 364
13X-RAY DIFFRACTION7D28 - 246
14X-RAY DIFFRACTION7D365 - 458
15X-RAY DIFFRACTION7D500 - 601
16X-RAY DIFFRACTION8D247 - 364

+
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