[English] 日本語
Yorodumi
- PDB-3lub: Crystal structure of Putative creatinine amidohydrolase (YP_21151... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lub
TitleCrystal structure of Putative creatinine amidohydrolase (YP_211512.1) from Bacteroides fragilis NCTC 9343 at 2.11 A resolution
ComponentsPutative creatinine amidohydrolase
KeywordsHYDROLASE / Putative creatinine amidohydrolase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


creatininase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / riboflavin biosynthetic process / metal ion binding
Similarity search - Function
Creatininase / Creatininase/formamide hydrolase / Creatininase-like superfamily / Creatinine amidohydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative creatinine amidohydrolase (YP_211512.1) from Bacteroides fragilis NCTC 9343 at 2.11 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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
Revision 1.5Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative creatinine amidohydrolase
B: Putative creatinine amidohydrolase
C: Putative creatinine amidohydrolase
D: Putative creatinine amidohydrolase
E: Putative creatinine amidohydrolase
F: Putative creatinine amidohydrolase
G: Putative creatinine amidohydrolase
H: Putative creatinine amidohydrolase
I: Putative creatinine amidohydrolase
J: Putative creatinine amidohydrolase
K: Putative creatinine amidohydrolase
L: Putative creatinine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)345,65672
Polymers342,46112
Non-polymers3,19460
Water40,0292222
1
A: Putative creatinine amidohydrolase
B: Putative creatinine amidohydrolase
C: Putative creatinine amidohydrolase
D: Putative creatinine amidohydrolase
E: Putative creatinine amidohydrolase
F: Putative creatinine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,91738
Polymers171,2316
Non-polymers1,68632
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31920 Å2
ΔGint-783 kcal/mol
Surface area50060 Å2
MethodPISA
2
G: Putative creatinine amidohydrolase
H: Putative creatinine amidohydrolase
I: Putative creatinine amidohydrolase
J: Putative creatinine amidohydrolase
K: Putative creatinine amidohydrolase
L: Putative creatinine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,73934
Polymers171,2316
Non-polymers1,50828
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31400 Å2
ΔGint-761 kcal/mol
Surface area49970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.906, 156.790, 170.161
Angle α, β, γ (deg.)90.000, 95.290, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MSE / Beg label comp-ID: MSE / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 2 / Auth seq-ID: 1 - 253 / Label seq-ID: 2 - 254

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL

-
Components

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Putative creatinine amidohydrolase


Mass: 28538.447 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: ATCC 25285 / NCTC 9343 / Gene: BF1877 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LE76

-
Non-polymers , 5 types, 2282 molecules

#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2222 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.2000M CaAcetate, 20.0000% PEG-3350, No Buffer pH 7.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97911
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 31, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.11→43.033 Å / Num. obs: 167009 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 25.198 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 8.25
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.11-2.190.5972.1663211762099.9
2.19-2.270.4912.6572771521199.9
2.27-2.380.43.2667231768299.9
2.38-2.50.3243.8603741593599.9
2.5-2.660.2554.8648751711299.9
2.66-2.860.1946.3615171621399.9
2.86-3.150.1338.8640801687799.9
3.15-3.60.08113.2626821653399.7
3.6-4.530.05618.1634781676399.6
4.53-43.0330.05919.4635701704199.5

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.11→43.033 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.695 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.227 / ESU R Free: 0.169
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 THE ...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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. DI-METALS (ZINC) AT ACTIVE SITES WERE CONFIRMED WITH X-RAY FLUORESCENE SPECTROSCOPY, ANOMALOUS DIFFERENCE FOURIERS AND COORDINATION GEOMETRY. 4.CALCIUM (CA), ETHYLENE GLYCOL (EDO) AND CHLORIDE (CL) MODELED WERE PRESENT IN CRYSTLLIZATION/CRYO CONDITIONS. 5. DUE TO THE THIN-SHELL SELECTION METHOD, THE HIGHEST SHELL DID NOT CONTAIN ANY FREE REFLECTIONS. THE 1137 REFLECTIONS IN THE SHELL 2.20-2.21 A HAD AN R-FREE OF 0.26.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 8604 5.2 %THIN SHELLS
Rwork0.151 ---
obs0.153 166973 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.31 Å2 / Biso mean: 25.45 Å2 / Biso min: 7.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å20.31 Å2
2---0.33 Å20 Å2
3----1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.11→43.033 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23844 0 93 2223 26160
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02224540
X-RAY DIFFRACTIONr_bond_other_d0.0010.0216448
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.95933372
X-RAY DIFFRACTIONr_angle_other_deg0.955340308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91253079
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.19824.5621107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.078154011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3121597
X-RAY DIFFRACTIONr_chiral_restr0.0860.23623
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0227463
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024762
X-RAY DIFFRACTIONr_nbd_refined0.1930.24827
X-RAY DIFFRACTIONr_nbd_other0.1880.216880
X-RAY DIFFRACTIONr_nbtor_refined0.1750.211500
X-RAY DIFFRACTIONr_nbtor_other0.0850.211768
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.21726
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0040.21
X-RAY DIFFRACTIONr_metal_ion_refined0.10.242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1650.232
X-RAY DIFFRACTIONr_mcbond_it1.631316045
X-RAY DIFFRACTIONr_mcbond_other0.2336118
X-RAY DIFFRACTIONr_mcangle_it2.242524564
X-RAY DIFFRACTIONr_scbond_it4.25810145
X-RAY DIFFRACTIONr_scangle_it5.691118782
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1442TIGHT POSITIONAL0.110.15
2B1442TIGHT POSITIONAL0.120.15
3C1442TIGHT POSITIONAL0.120.15
4D1442TIGHT POSITIONAL0.150.15
5E1442TIGHT POSITIONAL0.130.15
6F1442TIGHT POSITIONAL0.120.15
7G1442TIGHT POSITIONAL0.110.15
8H1442TIGHT POSITIONAL0.140.15
9I1442TIGHT POSITIONAL0.10.15
10J1442TIGHT POSITIONAL0.120.15
11K1442TIGHT POSITIONAL0.110.15
12L1442TIGHT POSITIONAL0.130.15
1A1695MEDIUM POSITIONAL0.230.6
2B1695MEDIUM POSITIONAL0.320.6
3C1695MEDIUM POSITIONAL0.310.6
4D1695MEDIUM POSITIONAL0.350.6
5E1695MEDIUM POSITIONAL0.30.6
6F1695MEDIUM POSITIONAL0.270.6
7G1695MEDIUM POSITIONAL0.260.6
8H1695MEDIUM POSITIONAL0.280.6
9I1695MEDIUM POSITIONAL0.260.6
10J1695MEDIUM POSITIONAL0.280.6
11K1695MEDIUM POSITIONAL0.330.6
12L1695MEDIUM POSITIONAL0.290.6
1A1442TIGHT THERMAL0.170.5
2B1442TIGHT THERMAL0.170.5
3C1442TIGHT THERMAL0.160.5
4D1442TIGHT THERMAL0.190.5
5E1442TIGHT THERMAL0.160.5
6F1442TIGHT THERMAL0.160.5
7G1442TIGHT THERMAL0.160.5
8H1442TIGHT THERMAL0.180.5
9I1442TIGHT THERMAL0.160.5
10J1442TIGHT THERMAL0.160.5
11K1442TIGHT THERMAL0.180.5
12L1442TIGHT THERMAL0.170.5
1A1695MEDIUM THERMAL1.052
2B1695MEDIUM THERMAL1.052
3C1695MEDIUM THERMAL1.062
4D1695MEDIUM THERMAL1.142
5E1695MEDIUM THERMAL1.072
6F1695MEDIUM THERMAL0.992
7G1695MEDIUM THERMAL1.062
8H1695MEDIUM THERMAL1.092
9I1695MEDIUM THERMAL1.032
10J1695MEDIUM THERMAL0.962
11K1695MEDIUM THERMAL1.132
12L1695MEDIUM THERMAL1.082
LS refinement shellResolution: 2.11→2.165 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.208 12400 -
obs--99.91 %

+
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