[English] 日本語
Yorodumi
- PDB-2b30: Initial Crystallographic Structural Analysis of a putative HAD/CO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2b30
TitleInitial Crystallographic Structural Analysis of a putative HAD/COF-like hydrolase from Plasmodium vivax
ComponentsPvivax hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SGPP / PSI / PROTEIN STRUCTURE INITIATIVE / Structural Genomics of Pathogenic Protozoa Consortium
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsRobien, M.A. / Bosch, J. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Initial Crystallographic Structural Analysis of a putative HAD/COF-like hydrolase from Plasmodium vivax
Authors: Robien, M.A. / Bosch, J. / Hol, W.G.J. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
History
DepositionSep 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). THE BIOLOGICAL UNIT IS NOT KNOWN, THE DIMERS (AB) AND (CD) ARE SUSPECTED BIOLOGICAL UNITS.
Remark 999SEQUENCE The sequence of this protein is not available at either SWS or GB sequence database at the ...SEQUENCE The sequence of this protein is not available at either SWS or GB sequence database at the time of processing. This protein is a homolog of Plasmodium falciparum PFL1270w, gi:23508948. The sequence is present in TargetDB as PVIV002324AAA, and in PlasmoDB v4.4 with gene identifier Pv_5271.phat_1. The N-terminus residues 1-8 are cloning artifacts.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Pvivax hypothetical protein
B: Pvivax hypothetical protein
C: Pvivax hypothetical protein
D: Pvivax hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,23112
Polymers136,9294
Non-polymers3028
Water1,928107
1
A: Pvivax hypothetical protein
B: Pvivax hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6156
Polymers68,4642
Non-polymers1514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Pvivax hypothetical protein
D: Pvivax hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6156
Polymers68,4642
Non-polymers1514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.101, 101.792, 97.337
Angle α, β, γ (deg.)90.00, 93.93, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Pvivax hypothetical protein / putative Cof-like hydrolase / HAD-superfamily / subfamily IIB


Mass: 34232.215 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax)
Plasmid: PET14B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: A5K063
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 8000, calcium chloride, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9739 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 13, 2005
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9739 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. all: 34235 / Num. obs: 34235 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 54.3 Å2 / Rsym value: 0.102 / Net I/σ(I): 8.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 4944 / Rsym value: 0.3 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1L6R, 1NF2, 1NRW, 1RKQ, 1TJ3, and 1RLM

1l6r

1nf2

1nrw

1rkq

1tj3

1rlm


Resolution: 2.7→37.24 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.852 / SU B: 13.216 / SU ML: 0.274 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25984 1726 5 %RANDOM
Rwork0.1968 ---
all0.20004 32477 --
obs0.20004 32477 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.151 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20.03 Å2
2---0.05 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.7→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9054 0 8 107 9169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0228910
X-RAY DIFFRACTIONr_bond_other_d0.0010.028036
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.95912079
X-RAY DIFFRACTIONr_angle_other_deg0.743318659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.93251136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.60625.684380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.17151529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0781512
X-RAY DIFFRACTIONr_chiral_restr0.0640.21417
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029946
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021714
X-RAY DIFFRACTIONr_nbd_refined0.2040.21874
X-RAY DIFFRACTIONr_nbd_other0.1680.28250
X-RAY DIFFRACTIONr_nbtor_refined0.1780.24423
X-RAY DIFFRACTIONr_nbtor_other0.0810.25179
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2264
X-RAY DIFFRACTIONr_metal_ion_refined0.1920.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.28
X-RAY DIFFRACTIONr_mcbond_it1.57745810
X-RAY DIFFRACTIONr_mcbond_other0.32542334
X-RAY DIFFRACTIONr_mcangle_it2.44769039
X-RAY DIFFRACTIONr_scbond_it2.763561
X-RAY DIFFRACTIONr_scangle_it4.052103038
LS refinement shellResolution: 2.7→2.845 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.332 253 -
Rwork0.23 4668 -
obs-4668 99.39 %

+
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