[English] 日本語
Yorodumi
- PDB-2ogi: Crystal structure of a putative metal dependent phosphohydrolase ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ogi
TitleCrystal structure of a putative metal dependent phosphohydrolase (sag1661) from streptococcus agalactiae serogroup v at 1.85 A resolution
ComponentsHypothetical protein SAG1661Hypothesis
KeywordsHYDROLASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


Ap4A hydrolase / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / GUANOSINE-5'-DIPHOSPHATE / HD domain-containing protein
Similarity search - Component
Biological speciesStreptococcus agalactiae serogroup V (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of conserved hypothetical protein TIGR00488 (NP_688652.1) from Streptococcus agalactiae 2603 at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: 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_conn_type / 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_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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). STATIC LIGHT SCATTERING WITH ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY MEASUREMENTS INDICATE THAT THE DIMER IS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE, FOLLOWED BY THE TARGET SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein SAG1661
B: Hypothetical protein SAG1661
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,59912
Polymers45,1882
Non-polymers1,41110
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-119 kcal/mol
Surface area17110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.841, 52.535, 70.022
Angle α, β, γ (deg.)90.000, 114.290, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TYRHIS5AA3 - 204 - 21
21TYRHIS5BB3 - 204 - 21
32MSELEU2AA21 - 6422 - 65
42MSELEU2BB21 - 6422 - 65
53SERGLY5AA65 - 8666 - 87
63SERGLY5BB65 - 8666 - 87
74ASNGLY2AA87 - 12088 - 121
84ASNGLY2BB87 - 12088 - 121
95SERTHR4AA121 - 126122 - 127
105SERTHR4BB121 - 126122 - 127
116LEUASN2AA127 - 140128 - 141
126LEUASN2BB127 - 140128 - 141
137ARGGLU5AA141 - 148142 - 149
147ARGGLU5BB141 - 148142 - 149
158ALAALA2AA149 - 173150 - 174
168ALAALA2BB149 - 173150 - 174
179SERGLN5AA174 - 177175 - 178
189SERGLN5BB174 - 177175 - 178
1910PROTYR2AA178 - 193179 - 194
2010PROTYR2BB178 - 193179 - 194

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Hypothetical protein SAG1661 / Hypothesis / conserved hypothetical protein TIGR00488


Mass: 22594.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serogroup V (bacteria)
Species: Streptococcus agalactiae / Strain: 2603 V/R / Gene: NP_688652.1, SAG1661 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DY32

-
Non-polymers , 5 types, 282 molecules

#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 277 K / pH: 6
Details: NANODROP, 1.0M LiCl, 20.0% PEG-6000, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP, pH 6.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97935, 0.97864
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 17, 2006 / Details: FLAT MIRROR (VERTICAL FOCUSING)
RadiationMonochromator: SINGLE CRYSTAL SI(111) BENT (HORIZONTAL FOCUSING)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979351
30.978641
ReflectionResolution: 1.85→40.555 Å / Num. obs: 37403 / % possible obs: 99.6 % / Biso Wilson estimate: 32.44 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 11.13
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 2 / % possible all: 98.9

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→40.55 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.677 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.135
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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. 4. EACH MONOMER CONTAINS TWO METALS WHICH ARE ASSIGNED AS FE. THE ASSIGNMENT OF FE IONS IS SUPPORTED BY BOTH X-RAY FLUORESCENCE EXCITATION SCAN AND ANOMALOUS DIFFERENCE FOURIER MAPS. 5. A GUANOSINE 5'-DIPHOSPHATE (GDP) MOLECULE WAS MODELED IN CHAINS A AND B NEAR THE DI-IRON SITE. THE ASSIGNMENT IS BASED ON THE DENSITY, PFAM ANNOTATION AND SIMILAR STRUCTURES. 6. SOME BLOBS OF ELECTRON DENSITY OUTSIDE PROTEIN REGION ARE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1865 5 %RANDOM
Rwork0.172 ---
obs0.174 37389 99.8 %-
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: 28.84 Å2
Baniso -1Baniso -2Baniso -3
1-1.6 Å20 Å2-1.2 Å2
2---0.27 Å20 Å2
3----2.32 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3089 0 75 272 3436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223269
X-RAY DIFFRACTIONr_bond_other_d0.0020.022937
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.9894449
X-RAY DIFFRACTIONr_angle_other_deg0.936823
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7345394
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08424.172151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10515556
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5761518
X-RAY DIFFRACTIONr_chiral_restr0.0940.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023598
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02660
X-RAY DIFFRACTIONr_nbd_refined0.2220.2805
X-RAY DIFFRACTIONr_nbd_other0.1780.22981
X-RAY DIFFRACTIONr_nbtor_refined0.1910.21635
X-RAY DIFFRACTIONr_nbtor_other0.0870.21858
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0490.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.05132000
X-RAY DIFFRACTIONr_mcbond_other0.6323793
X-RAY DIFFRACTIONr_mcangle_it3.02653134
X-RAY DIFFRACTIONr_scbond_it5.1881476
X-RAY DIFFRACTIONr_scangle_it7.054111313
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
779tight positional0.060.05
1567medium positional0.320.5
497loose positional0.875
779tight thermal0.350.5
1567medium thermal1.382
497loose thermal3.7110
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 132 -
Rwork0.266 2588 -
obs--98.69 %
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)
11.55760.0958-0.26941.12120.17643.529-0.09180.28760.0125-0.04050.0748-0.05090.3289-0.27020.017-0.1026-0.08470.0003-0.00560.0058-0.0464-2.952515.462230.8096
21.37140.14990.34241.35480.37212.14760.0377-0.16290.00770.0697-0.00710.12050.0189-0.4038-0.0306-0.0931-0.0107-0.0033-0.05810.0212-0.042-9.014228.147767.455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1944 - 195
2X-RAY DIFFRACTION2BB1 - 1942 - 195

+
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