[English] 日本語
Yorodumi
- PDB-5it4: Crystal structure of Mycobacterium avium SerB2 mutant D343N -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5it4
TitleCrystal structure of Mycobacterium avium SerB2 mutant D343N
ComponentsPhosphoserine phosphatase
KeywordsHYDROLASE / HAD family / phosphoserine phosphatase / catalytic site mutant
Function / homology
Function and homology information


phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / magnesium ion binding / cytoplasm
Similarity search - Function
: / ACT domain / ACT domain / haloacid dehalogenase-like hydrolase / Phosphoserine phosphatase / : / ACT domain / ACT domain profile. / ACT domain / ACT-like domain ...: / ACT domain / ACT domain / haloacid dehalogenase-like hydrolase / Phosphoserine phosphatase / : / ACT domain / ACT domain profile. / ACT domain / ACT-like domain / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoserine phosphatase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.102 Å
AuthorsShree, S. / Ramachandran, R.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific and Industrial Research (CSIR) India
Citation
Journal: To be published
Title: Crystal Structure of Mycobacterium avium SerB2 mutant D343N (MAV_3907) at pH 6.6
Authors: Shree, S. / Ramachandran, R.
#1: Journal: J. Struct. Funct. Genomics / Year: 2011
Title: SAD phasing using iodide ions in a high-throughput structural genomics environment.
Authors: Abendroth, J. / Gardberg, A.S. / Robinson, J.I. / Christensen, J.S. / Staker, B.L. / Myler, P.J. / Stewart, L.J. / Edwards, T.E.
History
DepositionMar 16, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8112
Polymers41,7871
Non-polymers241
Water2,990166
1
A: Phosphoserine phosphatase
hetero molecules

A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6224
Polymers83,5742
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6150 Å2
ΔGint-60 kcal/mol
Surface area30050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.035, 109.140, 134.024
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein Phosphoserine phosphatase / PSPase / O-phosphoserine phosphohydrolase


Mass: 41786.836 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 5-400 / Mutation: G31R, D343N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (strain 104) (bacteria)
Strain: 104 / Gene: serB, MAV_3907 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: A0QJI1, phosphoserine phosphatase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 22- 23% PEG 8000, 0.1 M Magnesium acetate tetrahydrate, 0.1 M HEPES pH 6.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 28166 / % possible obs: 98.6 % / Redundancy: 7.9 % / Net I/σ(I): 27.625

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P96

3p96


Resolution: 2.102→30.626 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 25.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2326 1999 7.1 %
Rwork0.1817 26149 -
obs0.1852 28148 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.82 Å2 / Biso mean: 47.5627 Å2 / Biso min: 27.27 Å2
Refinement stepCycle: final / Resolution: 2.102→30.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2855 0 1 166 3022
Biso mean--41.31 54.92 -
Num. residues----395
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072889
X-RAY DIFFRACTIONf_angle_d0.993940
X-RAY DIFFRACTIONf_chiral_restr0.04500
X-RAY DIFFRACTIONf_plane_restr0.004512
X-RAY DIFFRACTIONf_dihedral_angle_d11.9171026
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1022-2.15480.32021290.25271689181890
2.1548-2.2130.2751340.22861750188494
2.213-2.27810.27181390.20591811195096
2.2781-2.35160.26831400.19421829196998
2.3516-2.43570.20621450.182418962041100
2.4357-2.53310.21631430.184918722015100
2.5331-2.64840.24781430.184218762019100
2.6484-2.78790.2931440.199718792023100
2.7879-2.96240.25521440.202518812025100
2.9624-3.19090.25191460.189519062052100
3.1909-3.51160.23751440.180618932037100
3.5116-4.01880.20081470.160619182065100
4.0188-5.05960.17951470.149619322079100
5.0596-30.62880.251540.189220172171100
Refinement TLS params.Method: refined / Origin x: -5.095 Å / Origin y: -10.7597 Å / Origin z: -38.967 Å
111213212223313233
T0.3945 Å2-0.1814 Å20.0112 Å2-0.3366 Å2-0.011 Å2--0.337 Å2
L0.8043 °20.5309 °20.9857 °2-0.9289 °21.1058 °2--2.8641 °2
S0.0045 Å °0.0403 Å °-0.0668 Å °0.0063 Å °-0.0141 Å °0.024 Å °0.2227 Å °-0.0123 Å °0.0161 Å °
Refinement TLS groupSelection details: all

+
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