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- PDB-3dby: Crystal structure of uncharacterized protein from Bacillus cereus... -

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Basic information

Entry
Database: PDB / ID: 3dby
TitleCrystal structure of uncharacterized protein from Bacillus cereus G9241 (CSAP Target)
Componentsuncharacterized protein
Keywordsstructural genomics / unknown function / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyProtein of unknown function DUF2935 / Ferritin / Up-down Bundle / Mainly Alpha / : / :
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsRamagopal, U.A. / Bonanno, J.B. / Ozyurt, S. / Freeman, J. / Wasserman, S. / Hu, S. / Groshong, C. / Rodgers, L. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein from Bacillus cereus G9241
Authors: Ramagopal, U.A. / Bonanno, J.B. / Ozyurt, S. / Freeman, J. / Wasserman, S. / Hu, S. / Groshong, C. / Rodgers, L. / Burley, S.K. / Almo, S.C.
History
DepositionJun 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_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: uncharacterized protein
B: uncharacterized protein
C: uncharacterized protein
D: uncharacterized protein
E: uncharacterized protein
F: uncharacterized protein
G: uncharacterized protein
H: uncharacterized protein
I: uncharacterized protein
J: uncharacterized protein
K: uncharacterized protein
L: uncharacterized protein
M: uncharacterized protein
N: uncharacterized protein
O: uncharacterized protein
P: uncharacterized protein
Q: uncharacterized protein
R: uncharacterized protein
S: uncharacterized protein
T: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)630,72062
Polymers628,36220
Non-polymers2,35842
Water37,3452073
1
Q: uncharacterized protein
R: uncharacterized protein
hetero molecules

Q: uncharacterized protein
R: uncharacterized protein
hetero molecules

Q: uncharacterized protein
R: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,36521
Polymers188,5096
Non-polymers85615
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area22540 Å2
ΔGint-257 kcal/mol
Surface area58760 Å2
MethodPISA
2
E: uncharacterized protein
F: uncharacterized protein
hetero molecules

E: uncharacterized protein
F: uncharacterized protein
hetero molecules

E: uncharacterized protein
F: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,17918
Polymers188,5096
Non-polymers67012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area21840 Å2
ΔGint-266 kcal/mol
Surface area57390 Å2
MethodPISA
3
G: uncharacterized protein
H: uncharacterized protein
hetero molecules

G: uncharacterized protein
H: uncharacterized protein
hetero molecules

G: uncharacterized protein
H: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,17918
Polymers188,5096
Non-polymers67012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area21720 Å2
ΔGint-270 kcal/mol
Surface area57250 Å2
MethodPISA
4
K: uncharacterized protein
L: uncharacterized protein
hetero molecules

K: uncharacterized protein
L: uncharacterized protein
hetero molecules

K: uncharacterized protein
L: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,17918
Polymers188,5096
Non-polymers67012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area21700 Å2
ΔGint-264 kcal/mol
Surface area55440 Å2
MethodPISA
5
M: uncharacterized protein
N: uncharacterized protein
hetero molecules

M: uncharacterized protein
N: uncharacterized protein
hetero molecules

M: uncharacterized protein
N: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,17918
Polymers188,5096
Non-polymers67012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area21650 Å2
ΔGint-266 kcal/mol
Surface area55740 Å2
MethodPISA
6
A: uncharacterized protein
B: uncharacterized protein
hetero molecules

A: uncharacterized protein
B: uncharacterized protein
hetero molecules

A: uncharacterized protein
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,36521
Polymers188,5096
Non-polymers85615
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area22460 Å2
ΔGint-253 kcal/mol
Surface area57380 Å2
MethodPISA
7
I: uncharacterized protein
J: uncharacterized protein
hetero molecules

I: uncharacterized protein
J: uncharacterized protein
hetero molecules

I: uncharacterized protein
J: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,17918
Polymers188,5096
Non-polymers67012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area21780 Å2
ΔGint-268 kcal/mol
Surface area57210 Å2
MethodPISA
8
C: uncharacterized protein
D: uncharacterized protein
hetero molecules

C: uncharacterized protein
D: uncharacterized protein
hetero molecules

C: uncharacterized protein
D: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,17918
Polymers188,5096
Non-polymers67012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area21860 Å2
ΔGint-259 kcal/mol
Surface area59510 Å2
MethodPISA
9
O: uncharacterized protein
P: uncharacterized protein
hetero molecules

O: uncharacterized protein
P: uncharacterized protein
hetero molecules

O: uncharacterized protein
P: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,17918
Polymers188,5096
Non-polymers67012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area21570 Å2
ΔGint-267 kcal/mol
Surface area57120 Å2
MethodPISA
10
S: uncharacterized protein
T: uncharacterized protein
hetero molecules

S: uncharacterized protein
T: uncharacterized protein
hetero molecules

S: uncharacterized protein
T: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,17918
Polymers188,5096
Non-polymers67012
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area21930 Å2
ΔGint-261 kcal/mol
Surface area57480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.808, 167.808, 582.661
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
uncharacterized protein


Mass: 31418.086 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: G9241 / Gene: BCE_G9241_0798 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q4MWP8
#2: Chemical...
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2073 / 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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 24% PEG 3350, 0.2M Lithium acetate, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 346752 / Num. obs: 346752 / % possible obs: 97 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.161 / Rsym value: 0.093 / Χ2: 1.185 / Net I/σ(I): 10.7
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.9 / Num. unique all: 33933 / Rsym value: 0.645 / Χ2: 1.022 / % possible all: 94.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementResolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.381 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: UNKNOWN METALS HAVE BEEN MODELED AS "FE" BASED ON METALLOPROTEIN XAS SCREENING RESULTS AND OBSERVED ANOMALOUS FOURIER PEAKS.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 17434 5 %RANDOM
Rwork0.198 ---
all0.201 ---
obs0.201 345745 96.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.665 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43085 0 48 2073 45206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02244612
X-RAY DIFFRACTIONr_angle_refined_deg1.541.95260234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3255326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.74924.6492220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.138158296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.05615137
X-RAY DIFFRACTIONr_chiral_restr0.1010.26584
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02133417
X-RAY DIFFRACTIONr_mcbond_it0.7731.526348
X-RAY DIFFRACTIONr_mcangle_it1.463242489
X-RAY DIFFRACTIONr_scbond_it2.627318264
X-RAY DIFFRACTIONr_scangle_it4.2234.517701
LS refinement shellResolution: 2.098→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 1257 -
Rwork0.241 23324 -
all-24581 -
obs--92.42 %

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