[English] 日本語
Yorodumi
- PDB-4d9n: Crystal structure of Diaminopropionate ammonia lyase from Escheri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4d9n
TitleCrystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex with D-serine
ComponentsDiaminopropionate ammonia-lyase
KeywordsLYASE / Fold type II PLP-dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzymes superfamily
Function / homology
Function and homology information


diaminopropionate ammonia-lyase / diaminopropionate ammonia-lyase activity / pyridoxal phosphate binding / protein homodimerization activity
Similarity search - Function
Diaminopropionate ammonia-lyase / Diaminopropionate ammonia-lyase, subgroup / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-SERINE / Diaminopropionate ammonia-lyase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBisht, S. / Rajaram, V. / Bharath, S.R. / Murthy, M.R.N.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure of Escherichia coli Diaminopropionate Ammonia-lyase Reveals Mechanism of Enzyme Activation and Catalysis
Authors: Bisht, S. / Rajaram, V. / Bharath, S.R. / Kalyani, J.N. / Khan, F. / Rao, A.N. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionJan 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Database references
Revision 1.2May 10, 2017Group: Structure summary
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Diaminopropionate ammonia-lyase
B: Diaminopropionate ammonia-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4114
Polymers87,2012
Non-polymers2102
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-5 kcal/mol
Surface area27730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.611, 85.611, 207.652
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Diaminopropionate ammonia-lyase / Diaminopropionatase / Alpha / beta-diaminopropionate ammonia-lyase


Mass: 43600.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2871, JW2839, ygeX / Plasmid: pRSET-C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P66899, diaminopropionate ammonia-lyase
#2: Chemical ChemComp-DSN / D-SERINE


Type: D-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.18 Å3/Da / Density % sol: 43.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 20% PEG 3350, 70mM magnesium chloride, 50mM lithium sulfate, 6mM sodium citrate, 40mM tris HCl pH 8.3. Crystals were soaked with 10mM D-ser in crystallization condition for 10 hrs before ...Details: 20% PEG 3350, 70mM magnesium chloride, 50mM lithium sulfate, 6mM sodium citrate, 40mM tris HCl pH 8.3. Crystals were soaked with 10mM D-ser in crystallization condition for 10 hrs before data collection., VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 29, 2010 / Details: mirror
RadiationMonochromator: osmic mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 27635 / % possible obs: 99.8 % / Redundancy: 9.5 % / Biso Wilson estimate: 49.3 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 31.2
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 5 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1311 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D9I

4d9i


Resolution: 2.5→45.57 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.887 / SU B: 22.865 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.977 / ESU R Free: 0.328 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26738 1377 5 %RANDOM
Rwork0.21713 ---
obs0.21956 26023 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.121 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5907 0 14 101 6022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0196040
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9051.9548209
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4075777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87124.863255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00215947
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1391524
X-RAY DIFFRACTIONr_chiral_restr0.0580.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214572
X-RAY DIFFRACTIONr_gen_planes_other
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 75 -
Rwork0.288 1668 -
obs--96.94 %
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)
12.0027-0.00980.21840.45450.05810.89610.0467-0.0528-0.1717-0.1032-0.09050.09590.1864-0.11060.04380.1118-0.0259-0.0250.3296-0.04350.210123.69348.71974.336
23.24240.64450.25070.2769-0.36311.7733-0.0415-0.09460.1744-0.0186-0.05860.0916-0.0678-0.20230.10010.08360.0136-0.00880.2904-0.08130.210921.77955.56273.283
35.3909-0.4246-0.79322.52591.67091.93820.0949-0.4290.7055-0.0991-0.12040.3902-0.2756-0.22770.02550.0751-0.00330.03250.4804-0.13820.250720.39360.2887.264
42.25390.0495-0.9230.62180.48161.57810.0288-0.4310.150.0033-0.0727-0.0799-0.12410.03690.0440.094-0.0138-0.03570.4303-0.07550.209137.82157.3487.546
51.6735-0.19281.22610.866-0.35251.30140.14590.0178-0.09090.098-0.078-0.08130.19330.0022-0.06780.15030.0151-0.01540.2996-0.00150.178474.41946.53985.59
61.7563-0.39341.26730.4298-0.60752.2352-0.030.03180.17280.0446-0.1426-0.1611-0.09590.12170.17270.1102-0.017-0.00920.29380.00540.198876.42153.31285.846
70.10031.3842-0.212119.9809-3.11590.87260.2587-0.0558-0.11762.843-0.7389-2.309-0.83920.51690.48020.8345-0.4642-0.34640.65520.04490.692979.25565.03180.738
82.7370.0789-0.18810.4788-0.47231.1575-0.0406-0.1510.2469-0.019-0.09470.0339-0.06860.03340.13520.13390.0054-0.02430.3132-0.02350.198660.36759.00575.666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 143
2X-RAY DIFFRACTION2A144 - 244
3X-RAY DIFFRACTION3A245 - 302
4X-RAY DIFFRACTION4A303 - 397
5X-RAY DIFFRACTION5B2 - 145
6X-RAY DIFFRACTION6B146 - 263
7X-RAY DIFFRACTION7B264 - 302
8X-RAY DIFFRACTION8B303 - 397

+
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