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- PDB-3lub: Crystal structure of Putative creatinine amidohydrolase (YP_21151... -

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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


hydrolase activity / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A1 - 253
2112B1 - 253
3112C1 - 253
4112D1 - 253
5112E1 - 253
6112F1 - 253
7112G1 - 253
8112H1 - 253
9112I1 - 253
10112J1 - 253
11112K1 - 253
12112L1 - 253

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Components

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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

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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

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Details

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.

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Experimental details

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Experiment

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

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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

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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

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Phasing

PhasingMethod: SAD

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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 %

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