[English] 日本語
Yorodumi
- PDB-4rn3: Crystal structure of a HAD-superfamily hydrolase, subfamily IA, v... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rn3
TitleCrystal structure of a HAD-superfamily hydrolase, subfamily IA, variant 1 (GSU2069) from Geobacter sulfurreducens PCA at 2.15 A resolution
ComponentsHAD superfamily hydrolase
KeywordsHYDROLASE / PF13419 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


phosphoglycolate phosphatase activity / dephosphorylation / DNA repair / metal ion binding / cytosol
Similarity search - Function
Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
HAD superfamily hydrolase
Similarity search - Component
Biological speciesGeobacter sulfurreducens PCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a HAD-superfamily hydrolase, subfamily IA, variant 1 (GSU2069) from Geobacter sulfurreducens PCA at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HAD superfamily hydrolase
B: HAD superfamily hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2079
Polymers48,8482
Non-polymers3597
Water3,333185
1
A: HAD superfamily hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6355
Polymers24,4241
Non-polymers2114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HAD superfamily hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5734
Polymers24,4241
Non-polymers1483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.469, 190.593, 40.866
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein HAD superfamily hydrolase


Mass: 24424.184 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens PCA (bacteria)
Strain: ATCC 51573 / DSM 12127 / PCA / Gene: GSU2069 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q74BH2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (1-216) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (1-216) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 14.90% polyethylene glycol 3350 0.3570M magnesium chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.978662
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2008
Details: 2-crystal monochromator, Si111, 1m long Rh coated bent cylindrical mirror for horizontal and vertical focussing
RadiationMonochromator: 2-crystal, Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978662 Å / Relative weight: 1
ReflectionResolution: 2.15→39.958 Å / Num. obs: 25747 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.71 % / Biso Wilson estimate: 30.743 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 9.36
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.15-2.234.760.881.9512336259499.5
2.23-2.320.6782.512031251999.7
2.32-2.420.4893.311597240399.8
2.42-2.550.3774.112531259499.7
2.55-2.710.2955121552526100
2.71-2.920.2156.812389257699.9
2.92-3.210.12910.2120462523100
3.21-3.670.07415.812088258499.8
3.67-4.610.05320.611944260499.5
4.61-39.960.05721.512064282499.3

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJanuary 10, 2014 BUILT=20140307data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.15→39.958 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.9234 / Occupancy max: 1 / Occupancy min: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 FOR THE REDUCED ...Details: 1. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE SAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5.MAGNESIUM (MG) FROM THE CRYSTALLIZATION SOLUTION AND 1,2-ETHANEDIOL (EDO) USED AS A CRYOPROTECTANT WERE MODELED INTO THE STRUCTURE. 6. THERE IS GAP IN THE MODEL ON SUBUNIT B BETWEEN RESIDUES 62-71 SINCE ELECTRON DENSITIES FOR THESE RESIDUES ARE DISORDERED.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1310 5.1 %RANDOM
Rwork0.1987 ---
obs0.1996 25689 99.74 %-
Displacement parametersBiso max: 161.31 Å2 / Biso mean: 50.2337 Å2 / Biso min: 16.15 Å2
Baniso -1Baniso -2Baniso -3
1-4.5995 Å20 Å20 Å2
2---1.3908 Å20 Å2
3----3.2087 Å2
Refine analyzeLuzzati coordinate error obs: 0.313 Å
Refinement stepCycle: LAST / Resolution: 2.15→39.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3123 0 22 185 3330
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1562SINUSOIDAL10
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes506HARMONIC5
X-RAY DIFFRACTIONt_it3303HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC10
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion422SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3951SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3303HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4472HARMONIC100.35
X-RAY DIFFRACTIONt_omega_torsion4.28
X-RAY DIFFRACTIONt_other_torsion1.91
LS refinement shellResolution: 2.15→2.24 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2103 144 5.11 %
Rwork0.2242 2673 -
all0.2235 2817 -
obs--99.74 %
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)
10.7771-0.26980.05850.6733-0.18321.0208-0.04770.0359-0.03160.05670.0343-0.01980.0571-0.0770.0134-0.1437-0.00350.0123-0.0524-0.04070.068512.614341.158226.1697
24.76032.98740.61475.24071.46771.97660.15570.0647-1.0885-0.0640.0035-0.69990.2441-0.0445-0.1592-0.2680.0221-0.0513-0.3395-0.01030.274629.502115.282216.5734
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 212
2X-RAY DIFFRACTION2B9 - 211

+
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