[English] 日本語
Yorodumi
- PDB-7ea4: Crystal Structure of L182E D-Succinylase (DSA) from Cupriavidus s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ea4
TitleCrystal Structure of L182E D-Succinylase (DSA) from Cupriavidus sp. P4-10-C
ComponentsD-succinylase
KeywordsHYDROLASE / D-Succinylase / Cupriavidus sp.
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / antibiotic biosynthetic process / metal ion binding
Similarity search - Function
Penicillin/GL-7-ACA/AHL acylase / Penicillin/GL-7-ACA/AHL/aculeacin-A acylase / Penicillin amidase type, domain 1 / Penicillin amidase type, N-terminal domain, B-knob / Penicillin amidase type, A-knob / Penicillin amidase / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
CACODYLIC ACID / CARBONATE ION / SUCCINIC ACID / D-succinylase
Similarity search - Component
Biological speciesCupriavidus sp. P4-10-C (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsYamasaki, M. / Sumida, Y.
CitationJournal: Adv.Synth.Catal. / Year: 2021
Title: Protein Engineering of d-Succinylase from Cupriavidus sp. for d-Amino Acid Synthesis and the Structural Implications.
Authors: Sumida, Y. / Yamasaki, M. / Nishiya, Y. / Kumagai, S. / Yamada, T. / Azuma, M.
History
DepositionMar 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: D-succinylase
B: D-succinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,93616
Polymers181,6752
Non-polymers1,26214
Water15,619867
1
A: D-succinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,66910
Polymers90,8371
Non-polymers8329
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area27710 Å2
MethodPISA
2
B: D-succinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2676
Polymers90,8371
Non-polymers4305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-12 kcal/mol
Surface area27590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.057, 129.806, 200.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 36 through 131 or resid 133...
d_2ens_1(chain "B" and (resid 36 through 131 or resid 133...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1THRLYSA1 - 96
d_12ens_1VALSERA98 - 132
d_13ens_1TRPALAA134 - 136
d_14ens_1ASPCYSA138 - 162
d_15ens_1ALAALAA164 - 169
d_16ens_1ALAPROA171 - 187
d_17ens_1GLYTRPA189 - 218
d_18ens_1SERLEUA220 - 261
d_19ens_1VALTRPA263 - 411
d_110ens_1PROTRPA413 - 480
d_111ens_1ASPALAA482 - 486
d_112ens_1ARGGLNA488 - 542
d_113ens_1ALAPHEA544 - 569
d_114ens_1ASNVALA571 - 578
d_115ens_1ALAGLUA580 - 584
d_116ens_1ALAGLUA586 - 630
d_117ens_1ARGTYRA632 - 727
d_118ens_1ASPARGA729 - 762
d_21ens_1THRLYSF1 - 96
d_22ens_1VALSERF98 - 132
d_23ens_1TRPALAF134 - 136
d_24ens_1ASPCYSF138 - 162
d_25ens_1ALAALAF164 - 169
d_26ens_1ALAPROF171 - 187
d_27ens_1GLYLEUF189 - 260
d_28ens_1VALTRPF262 - 410
d_29ens_1PROTRPF412 - 479
d_210ens_1ASPALAF481 - 485
d_211ens_1ARGGLNF487 - 541
d_212ens_1ALAPHEF543 - 568
d_213ens_1ASNVALF570 - 577
d_214ens_1ALAGLUF579 - 583
d_215ens_1ALAGLUF585 - 629
d_216ens_1ARGTYRF631 - 726
d_217ens_1ASPARGF728 - 761

NCS oper: (Code: givenMatrix: (-0.756288281674, 0.604174745012, -0.250999825682), (0.610213433808, 0.513060179565, -0.603662834159), (-0.235939823266, -0.609706593071, -0.756696947373)Vector: -50. ...NCS oper: (Code: given
Matrix: (-0.756288281674, 0.604174745012, -0.250999825682), (0.610213433808, 0.513060179565, -0.603662834159), (-0.235939823266, -0.609706593071, -0.756696947373)
Vector: -50.6704892938, 89.4440441558, 172.491338319)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein D-succinylase


Mass: 90837.398 Da / Num. of mol.: 2 / Mutation: L182E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus sp. P4-10-C (bacteria) / Gene: DSA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N7KZ58

-
Non-polymers , 7 types, 881 molecules

#2: Chemical ChemComp-CAD / CACODYLIC ACID / HYDROXYDIMETHYLARSINE OXIDE / Cacodylic acid


Mass: 137.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H7AsO2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CO3 / CARBONATE ION / Carbonate


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 867 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: 11% PEG 8000, 0.1M Sodium cacodylate, 0.2M MaCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jun 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 118124 / % possible obs: 99.6 % / Redundancy: 4.7 % / CC1/2: 0.993 / CC star: 0.998 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.051 / Rrim(I) all: 0.112 / Net I/σ(I): 11
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 4.5 % / Num. unique obs: 5812 / CC1/2: 0.821 / CC star: 0.949 / Rpim(I) all: 0.284 / Rrim(I) all: 0.619 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DENZOdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HST

4hst


Resolution: 1.95→42.93 Å / SU ML: 0.1955 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.0063
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.208 5909 5.01 %
Rwork0.1644 112118 -
obs0.1666 118027 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.79 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11879 0 70 867 12816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007112416
X-RAY DIFFRACTIONf_angle_d0.88116949
X-RAY DIFFRACTIONf_chiral_restr0.05631770
X-RAY DIFFRACTIONf_plane_restr0.00952257
X-RAY DIFFRACTIONf_dihedral_angle_d12.53584513
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.536200625608 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.28241850.21883499X-RAY DIFFRACTION94.32
1.97-20.24752050.20953740X-RAY DIFFRACTION99.95
2-2.020.2741960.20143647X-RAY DIFFRACTION99.95
2.02-2.050.28381650.20253738X-RAY DIFFRACTION99.95
2.05-2.070.24972140.19823726X-RAY DIFFRACTION99.82
2.07-2.10.25261780.19163717X-RAY DIFFRACTION99.92
2.1-2.130.25882070.18473701X-RAY DIFFRACTION99.87
2.13-2.160.22661980.17943716X-RAY DIFFRACTION99.97
2.16-2.20.24251970.17553691X-RAY DIFFRACTION99.95
2.2-2.230.22042190.17493716X-RAY DIFFRACTION99.9
2.23-2.270.23141880.17723704X-RAY DIFFRACTION99.85
2.27-2.310.22172010.17053737X-RAY DIFFRACTION99.87
2.31-2.360.22881890.17443734X-RAY DIFFRACTION99.95
2.36-2.410.21312210.16963704X-RAY DIFFRACTION99.85
2.41-2.460.24472070.17183706X-RAY DIFFRACTION99.92
2.46-2.520.23091900.1733736X-RAY DIFFRACTION99.7
2.52-2.580.24482130.17733716X-RAY DIFFRACTION99.82
2.58-2.650.22931950.17893729X-RAY DIFFRACTION99.87
2.65-2.730.22922080.17323743X-RAY DIFFRACTION99.75
2.73-2.810.20612110.17443729X-RAY DIFFRACTION99.62
2.81-2.910.21671900.17513727X-RAY DIFFRACTION99.69
2.91-3.030.22221840.17483770X-RAY DIFFRACTION99.62
3.03-3.170.23391660.17743763X-RAY DIFFRACTION99.37
3.17-3.340.2052240.16823745X-RAY DIFFRACTION99.32
3.34-3.550.18851870.1513746X-RAY DIFFRACTION99.14
3.55-3.820.17172000.13743767X-RAY DIFFRACTION99.2
3.82-4.20.15531750.1413802X-RAY DIFFRACTION98.68
4.2-4.810.1561850.12443816X-RAY DIFFRACTION98.96
4.81-6.060.17372130.14773839X-RAY DIFFRACTION99.48
6.06-42.930.16481980.14614014X-RAY DIFFRACTION98.64

+
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