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- PDB-4s1a: Crystal structure of a hypothetical protein Cthe_0052 from Rumini... -

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Basic information

Entry
Database: PDB / ID: 4s1a
TitleCrystal structure of a hypothetical protein Cthe_0052 from Ruminiclostridium thermocellum ATCC 27405
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homologyPutative glycosyl hydrolase domain DUF4015 / Putative glycosyl hydrolase domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / CITRATE ANION / DUF4015 domain-containing protein
Function and homology information
Biological speciesRuminiclostridium thermocellum ATCC 27405 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Minasov, G. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical protein Cthe_0052 from Ruminiclostridium thermocellum ATCC27405
Authors: Filippova, E.V. / Wawrzak, Z. / Minasov, G. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionJan 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5585
Polymers53,0532
Non-polymers5053
Water8,251458
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-9 kcal/mol
Surface area17620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.539, 65.483, 113.021
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein


Mass: 26526.379 Da / Num. of mol.: 2 / Fragment: UNP residues 94-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminiclostridium thermocellum ATCC 27405 (bacteria)
Strain: ATCC 27405 / Gene: Cthe_0052 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: A3DBG4
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M Na Citrate, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 14, 2014 / Details: beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 44613 / Num. obs: 44613 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 32.4
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.8.0069refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.444 / SU ML: 0.072 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19775 2155 4.8 %RANDOM
Rwork0.15913 ---
obs0.161 42391 99.9 %-
all-42391 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.861 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20 Å20 Å2
2---2.35 Å2-0 Å2
3---0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3074 0 30 458 3562
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193205
X-RAY DIFFRACTIONr_bond_other_d0.0010.022993
X-RAY DIFFRACTIONr_angle_refined_deg1.6451.9494346
X-RAY DIFFRACTIONr_angle_other_deg0.8436894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.185382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.9524.783161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.4715528
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.811514
X-RAY DIFFRACTIONr_chiral_restr0.1070.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023630
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02748
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_it1.4811.5731531
X-RAY DIFFRACTIONr_mcbond_other1.4811.571530
X-RAY DIFFRACTIONr_mcangle_it2.292.3441912
X-RAY DIFFRACTIONr_mcangle_other2.2892.3471913
X-RAY DIFFRACTIONr_scbond_it2.4471.9151674
X-RAY DIFFRACTIONr_scbond_other2.4191.9161674
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7072.7512435
X-RAY DIFFRACTIONr_long_range_B_refined7.46115.6784125
X-RAY DIFFRACTIONr_long_range_B_other7.4615.6864126
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 141 -
Rwork0.219 3105 -
obs--99.94 %
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)
11.63051.68861.13694.77421.74293.9736-0.15340.04140.2588-0.40720.02760.6321-0.1625-0.28270.12580.05810.0206-0.04620.08520.00570.144745.129976.9016150.8186
21.74720.21020.70822.6294-0.09731.283-0.0914-0.0651-0.02820.13960.04260.10450.0264-0.03820.04870.04220.01260.04070.05980.01490.043557.306976.8248160.5288
31.81021.5680.75162.69830.59740.8807-0.0922-0.0017-0.03180.06590.05230.07290.04770.02040.040.04210.01380.01110.0358-0.00090.03160.546277.359157.6633
41.49950.62220.03752.10380.39880.8483-0.10350.0261-0.02440.07680.0825-0.1562-0.02460.06060.0210.02110.0063-0.01270.04570.01160.027770.169282.4548157.7519
52.08240.70310.23673.34561.82861.0755-0.11830.1501-0.0318-0.28090.2351-0.3505-0.14570.1531-0.11680.0604-0.03980.01120.1391-0.00840.155479.884483.0232151.5219
62.5322-0.3799-0.18632.3518-2.05243.3845-0.13510.1722-0.120.37870.032-0.1675-0.36060.06690.10310.0728-0.0218-0.01650.0624-0.02990.056671.12273.8998147.1302
72.198-1.7148-1.27743.81741.19422.3136-0.05810.0809-0.34320.142-0.02570.60880.0733-0.19480.08380.0217-0.01490.00270.0655-0.00680.158447.190476.4621129.3821
82.2174-1.3634-0.61332.76150.12851.27980.0560.13050.0241-0.1203-0.04610.2273-0.0805-0.0864-0.00980.0144-0.0006-0.01660.0395-0.00260.045557.407879.0139124.5463
91.3805-0.37390.12594.0159-0.15471.48190.01610.0015-0.0105-0.24830.0154-0.10120.07820.074-0.03150.02590.00630.01450.0544-0.00030.016975.352965.7634123.2278
101.9983-1.0237-0.43752.41980.72770.5862-0.0786-0.10350.14450.10730.1061-0.22160.03790.1387-0.02750.01960.0080.00030.0784-0.01430.041674.489474.5728131.016
112.05762.0365-1.92132.7339-3.60176.1066-0.1068-0.18810-0.314-0.1117-0.14360.51010.1410.21850.1137-0.02060.05620.1348-0.04740.138370.655580.9496135.964
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A94 - 117
2X-RAY DIFFRACTION2A118 - 156
3X-RAY DIFFRACTION3A157 - 190
4X-RAY DIFFRACTION4A191 - 241
5X-RAY DIFFRACTION5A242 - 270
6X-RAY DIFFRACTION6A271 - 287
7X-RAY DIFFRACTION7B94 - 116
8X-RAY DIFFRACTION8B117 - 174
9X-RAY DIFFRACTION9B175 - 219
10X-RAY DIFFRACTION10B220 - 271
11X-RAY DIFFRACTION11B272 - 285

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