[English] 日本語
Yorodumi
- PDB-2hi0: Crystal structure of putative phosphoglycolate phosphatase (YP_61... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hi0
TitleCrystal structure of putative phosphoglycolate phosphatase (YP_619066.1) from Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 at 1.51 A resolution
ComponentsPutative phosphoglycolate phosphatase
KeywordsHYDROLASE / YP_619066.1 / putative / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


phosphoglycolate phosphatase / phosphoglycolate phosphatase activity
Similarity search - Function
Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Putative phosphoglycolate phosphatase
Similarity search - Component
Biological speciesLactobacillus delbrueckii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.51 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of putative phosphoglycolate phosphatase (YP_619066.1) from Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365 at 1.51 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE SEQUENCE DIFFERENCE ARISES BECAUSE THE PROTEIN WAS OBTAINED FROM A DIFFERENT ...SEQUENCE THE SEQUENCE DIFFERENCE ARISES BECAUSE THE PROTEIN WAS OBTAINED FROM A DIFFERENT SUBSPECIES (ATCC BAA-365). THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative phosphoglycolate phosphatase
B: Putative phosphoglycolate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,63926
Polymers53,3232
Non-polymers1,31724
Water11,476637
1
A: Putative phosphoglycolate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,20711
Polymers26,6611
Non-polymers54610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative phosphoglycolate phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,43215
Polymers26,6611
Non-polymers77114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.636, 38.695, 103.583
Angle α, β, γ (deg.)90.000, 98.090, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Putative phosphoglycolate phosphatase /


Mass: 26661.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus delbrueckii (bacteria) / Gene: YP_619066.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1GA24, phosphoglycolate phosphatase

-
Non-polymers , 5 types, 661 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 43.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6.5
Details: 0.2M NaOAc, 30.0% PEG-8000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97939
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 4, 2006 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979391
ReflectionResolution: 1.51→47.727 Å / Num. obs: 72271 / % possible obs: 95.8 % / Redundancy: 3.61 % / Biso Wilson estimate: 19.143 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 8.75
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.51-1.562.770.5372.115640557582.6
1.56-1.630.5152.627140755093.2
1.63-1.70.4483.123957643994.6
1.7-1.790.3653.825809695895.7
1.79-1.90.2734.925745690496.6
1.9-2.050.1847.126987723597.6
2.05-2.250.1211026070701598.9
2.25-2.580.09212.627493736599.1
2.580.06815.727229731699.3

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.51→47.727 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.969 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.075
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3) NA, CL, ACT AND EDO WERE MODELLED BASED ON CRYSTALLIZATION CONDITIONS AND THEIR GEOMETRY. (4) ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 3644 5 %RANDOM
Rwork0.157 ---
all0.158 ---
obs0.158 72257 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.423 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.19 Å2
2--0.17 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.51→47.727 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3675 0 81 637 4393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223881
X-RAY DIFFRACTIONr_bond_other_d0.0020.022642
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.975239
X-RAY DIFFRACTIONr_angle_other_deg0.9936458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4875499
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.54724.588170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06315653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4441522
X-RAY DIFFRACTIONr_chiral_restr0.0930.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02765
X-RAY DIFFRACTIONr_nbd_refined0.2290.2791
X-RAY DIFFRACTIONr_nbd_other0.1960.22810
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21920
X-RAY DIFFRACTIONr_nbtor_other0.0860.21893
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2440
X-RAY DIFFRACTIONr_metal_ion_refined0.2080.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2890.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.254
X-RAY DIFFRACTIONr_mcbond_it1.70732443
X-RAY DIFFRACTIONr_mcbond_other0.5323987
X-RAY DIFFRACTIONr_mcangle_it2.63253944
X-RAY DIFFRACTIONr_scbond_it4.4381458
X-RAY DIFFRACTIONr_scangle_it6.563111289
LS refinement shellResolution: 1.51→1.549 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 245 -
Rwork0.25 4637 -
obs-4882 90.69 %
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)
10.7617-0.3193-0.36090.782-0.18280.8631-0.0221-0.0479-0.04860.0281-0.0021-0.02330.07650.11460.0242-0.00130.02260.0085-0.01330.0025-0.0116.23236.873936.148
20.8183-0.1945-0.00530.6940.28261.2497-0.0240.029-0.04940.01250.01820.07470.0058-0.06640.0058-0.045-0.00220.0045-0.04010.0043-0.0269-14.163917.126437.0173
30.6629-0.1499-0.12350.34740.09931.07250.00470.0287-0.0163-0.01850.01520.0035-0.0255-0.0342-0.02-0.0332-0.0057-0.0032-0.0238-0.0043-0.015510.9925-14.46169.2787
40.42-0.0293-0.27590.4741-0.15191.294-0.0176-0.0103-0.03920.0117-0.0127-0.0457-0.02430.03860.0303-0.0505-0.0053-0.007-0.026-0.0008-0.022330.5584-3.470815.4184
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 161 - 17
21AA109 - 239110 - 240
32AA17 - 10818 - 109
43BB3 - 164 - 17
53BB109 - 239110 - 240
64BB17 - 10818 - 109

+
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