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- PDB-3fgx: Structure of uncharacterised protein rbstp2171 from bacillus stea... -

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Basic information

Entry
Database: PDB / ID: 3fgx
TitleStructure of uncharacterised protein rbstp2171 from bacillus stearothermophilus
ComponentsRBSTP2171
Keywordsstructural genomics / unknown function / BACILLUS STEAROTHERMOPHILUS / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyrbstp2171 / rbstp2171 / 2-Layer Sandwich / Alpha Beta
Function and homology information
Biological speciesBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsMinasov, G. / Filippova, E.V. / Shuvalova, L. / Moy, S. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of Uncharacterised Protein Rbstp2171 from Bacillus Stearothermophilus
Authors: Minasov, G. / Filippova, E.V. / Shuvalova, L. / Moy, S. / Joachimiak, A. / Anderson, W.F.
History
DepositionDec 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RBSTP2171
B: RBSTP2171


Theoretical massNumber of molelcules
Total (without water)26,0182
Polymers26,0182
Non-polymers00
Water905
1
A: RBSTP2171


Theoretical massNumber of molelcules
Total (without water)13,0091
Polymers13,0091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RBSTP2171


Theoretical massNumber of molelcules
Total (without water)13,0091
Polymers13,0091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.099, 89.099, 31.599
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain: (Details: A B)
NCS domain segments:

Dom-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 1 / Auth seq-ID: 9 - 112 / Label seq-ID: 9 - 112

Component-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein RBSTP2171


Mass: 13008.776 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS STEAROTHERMOPHILUS (bacteria) / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.42 Å3/Da / Density % sol: 49.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES sodium salt, 2% PEG 400, 2.0 M Ammonium sulfate , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97869 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 28, 2007 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 2.9→89.09 Å / Num. all: 5778 / Num. obs: 5778 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 25.96
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.501 / % possible all: 100

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Processing

Software
NameVersionClassification
SHARPphasing
ARP/wARPmodel building
Omodel building
REFMAC5.5.0051refinement
Blu-IceMaxdata collection
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.9→89.09 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.909 / SU B: 50.497 / SU ML: 0.39 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.439 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.279 262 4.6 %RANDOM
Rwork0.255 ---
obs0.256 5723 --
all-5723 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.43 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20 Å2
2--1.61 Å20 Å2
3----3.22 Å2
Refinement stepCycle: LAST / Resolution: 2.9→89.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1538 0 0 5 1543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221563
X-RAY DIFFRACTIONr_bond_other_d0.0020.021110
X-RAY DIFFRACTIONr_angle_refined_deg1.7711.9742097
X-RAY DIFFRACTIONr_angle_other_deg0.96932697
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7055188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.33224.21176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.18815293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7741512
X-RAY DIFFRACTIONr_chiral_restr0.090.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211706
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02322
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_it0.3752956
X-RAY DIFFRACTIONr_mcbond_other0.0732382
X-RAY DIFFRACTIONr_mcangle_it0.66731542
X-RAY DIFFRACTIONr_scbond_it0.5112607
X-RAY DIFFRACTIONr_scangle_it0.9454555
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 / Number: 1312 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.010.05
TIGHT THERMAL0.020.5
LS refinement shellResolution: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.459 19 -
Rwork0.358 400 -
obs--100 %
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)
110.2478-0.5479-3.24082.5535-0.48174.24130.3121-0.0914-0.08560.1103-0.24310.4574-0.315-0.1176-0.0690.2043-0.1141-0.00070.1146-0.02680.0921-12.8157-11.9748-2.2057
22.2962-0.9621-0.268610.3466-2.92693.7164-0.27270.1440.4127-0.09680.3472-0.0772-0.1319-0.3714-0.07450.1361-0.1206-0.0380.21170.0150.0811-32.5531-31.6421-10.4455
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 112
2X-RAY DIFFRACTION2B9 - 112

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