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- PDB-3fq3: Crystal structure of inorganic phosphatase from brucella melitensis -

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Basic information

Entry
Database: PDB / ID: 3fq3
TitleCrystal structure of inorganic phosphatase from brucella melitensis
ComponentsInorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
KeywordsHYDROLASE / SSGCID / INORGANIC PHOSPHATASE / BRUCELLA MELITENSIS / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Inorganic Pyrophosphatase / Inorganic pyrophosphatase / Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Inorganic pyrophosphatase
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus 2308 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of inorganic phosphatase from brucella melitensis
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJan 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
B: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
C: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
D: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
E: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
F: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
G: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
H: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
I: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
J: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
K: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
L: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,63033
Polymers265,63512
Non-polymers1,99421
Water36,9852053
1
A: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
B: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
C: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
D: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
E: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
F: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,95718
Polymers132,8186
Non-polymers1,14012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
G: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
H: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
I: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
J: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
K: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
L: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,67215
Polymers132,8186
Non-polymers8559
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
C: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
E: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9799
Polymers66,4093
Non-polymers5706
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-62 kcal/mol
Surface area22000 Å2
MethodPISA
4
B: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
D: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
F: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9799
Polymers66,4093
Non-polymers5706
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-59 kcal/mol
Surface area22210 Å2
MethodPISA
5
H: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
J: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
L: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8848
Polymers66,4093
Non-polymers4755
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-56 kcal/mol
Surface area22160 Å2
MethodPISA
6
G: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
I: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
K: Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7897
Polymers66,4093
Non-polymers3804
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-51 kcal/mol
Surface area21730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.830, 157.830, 106.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
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
1116A1 - 175
2116B1 - 175
3116C1 - 175
4116D1 - 175
5116E1 - 175
6116F1 - 175
7116G1 - 175
8116H1 - 175
9116I1 - 175
10116J1 - 175
11116K1 - 175
12116L1 - 175
DetailsBIOLOGICAL UNIT IS A HEXAMER FORMED BY SUBUNITS A-F AND G-L.

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Components

#1: Protein
Inorganic pyrophosphatase:Bacterial/Archaeal inorganic pyrophosphatase


Mass: 22136.264 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biovar Abortus 2308 (bacteria)
Strain: BIOVAR ABORTUS 2308 / Gene: ppa, BAB1_1993 / Plasmid: AVA0421 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YR76, inorganic diphosphatase
#2: Chemical...
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2053 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: HAMPTON SALT RX SCREEN E9: 1.8M K2HPO4/NAH2PO4 PH 6.9, PH 5.5, VAPOR DIFFUSION, TEMPERATURE 290K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1
DetectorType: NOIR-1 / Detector: CCD / Date: Oct 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 204887 / Num. obs: 204646 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / Biso Wilson estimate: 29.95 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 22.57
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.475 / Mean I/σ(I) obs: 4.6 / Num. unique all: 15077 / Rsym value: 0.475 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0070refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3d53 as hexamer, sidechains trimmed with chainsaw

3d53


Resolution: 1.9→19.87 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.851 / SU ML: 0.085 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.209 10354 5.1 %RANDOM
Rwork0.167 ---
obs0.169 204605 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20 Å2
2---0.18 Å20 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16227 0 105 2053 18385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02216826
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211233
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.97822998
X-RAY DIFFRACTIONr_angle_other_deg0.949327558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0352103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84924.407742
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.381152668
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3241589
X-RAY DIFFRACTIONr_chiral_restr0.1010.22541
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02118656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023172
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.051.510475
X-RAY DIFFRACTIONr_mcbond_other0.2861.54146
X-RAY DIFFRACTIONr_mcangle_it1.862217109
X-RAY DIFFRACTIONr_scbond_it2.8136351
X-RAY DIFFRACTIONr_scangle_it4.5414.55873
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2115 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.475
2Bloose positional0.495
3Cloose positional0.515
4Dloose positional0.495
5Eloose positional0.465
6Floose positional0.485
7Gloose positional0.475
8Hloose positional0.485
9Iloose positional0.435
10Jloose positional0.485
11Kloose positional0.385
12Lloose positional0.395
1Aloose thermal3.7110
2Bloose thermal3.4810
3Cloose thermal3.8510
4Dloose thermal2.610
5Eloose thermal2.2410
6Floose thermal3.310
7Gloose thermal6.2610
8Hloose thermal3.9910
9Iloose thermal6.4410
10Jloose thermal3.310
11Kloose thermal2.6910
12Lloose thermal2.7710
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 750 -
Rwork0.207 14189 -
obs--100 %

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