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- PDB-4z8z: Crystal structure of the hypothetical protein from Ruminiclostrid... -

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Basic information

Entry
Database: PDB / ID: 4z8z
TitleCrystal structure of the hypothetical protein from Ruminiclostridium thermocellum ATCC 27405
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / Structural Genomics / Human Microbiome / Midwest Center For Structural Genomics / MCSG / PSI-Biology
Function / homologyAlpha/Beta hydrolase fold / Alpha/beta hydrolase
Function and homology information
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
AuthorsFilippova, E.V. / Wawrzak, Z. / Kiryukhina, O. / Endres, M. / Joachimiak, J. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal structure of the hypothetical protein from Ruminiclostridium thermocellum ATCC 27405
Authors: Filippova, E.V. / Wawrzak, Z. / Kiryukhina, O. / Endres, M. / Joachimiak, J. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionApr 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: audit_author / entity_src_gen ...audit_author / entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
Item: _audit_author.name / _entity_src_gen.pdbx_alt_source_flag ..._audit_author.name / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)38,0501
Polymers38,0501
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)141.353, 141.353, 112.676
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Uncharacterized protein


Mass: 38050.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (strain ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372) (bacteria)
Strain: ATCC 27405 / DSM 1237 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372
Gene: Cthe_0134 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / References: UniProt: A3DBP6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Trimethylamine N-oxide, 0.1 M Tris, 20% PEG2000

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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: Nov 24, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.55→30 Å / Num. all: 14192 / Num. obs: 14192 / % possible obs: 99.9 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 51.7
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
BLU-MAXdata collection
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.55→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.949 / SU B: 21.269 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.433 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22171 694 4.9 %RANDOM
Rwork0.17505 13496 --
obs0.17745 13496 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.527 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å2-1.01 Å20 Å2
2---2.02 Å20 Å2
3---6.56 Å2
Refinement stepCycle: 1 / Resolution: 2.55→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 0 27 2646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192675
X-RAY DIFFRACTIONr_bond_other_d0.0020.022590
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.9833607
X-RAY DIFFRACTIONr_angle_other_deg1.01635959
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2765318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9124.545132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.50515463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.91513
X-RAY DIFFRACTIONr_chiral_restr0.0980.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022984
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02627
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_it2.0654.3891278
X-RAY DIFFRACTIONr_mcbond_other2.0644.3871277
X-RAY DIFFRACTIONr_mcangle_it3.256.5761594
X-RAY DIFFRACTIONr_mcangle_other3.2496.5781595
X-RAY DIFFRACTIONr_scbond_it2.4934.6541397
X-RAY DIFFRACTIONr_scbond_other2.4934.6561398
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9226.8662014
X-RAY DIFFRACTIONr_long_range_B_refined5.32734.3232903
X-RAY DIFFRACTIONr_long_range_B_other5.32334.3312903
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.551→2.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 49 -
Rwork0.257 970 -
obs--97.33 %
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)
12.1125-1.6498-0.68558.99121.08190.3007-0.09-0.0797-0.1656-0.19450.00470.1604-0.05960.11190.08540.2857-0.0854-0.04960.2760.03240.0654106.6335133.5031123.8781
23.00930.6996-0.03281.42830.50673.429-0.0673-0.078-0.6175-0.32790.001-0.04320.39650.13260.06620.20160.0405-0.01820.03840.02160.142996.955108.2275130.769
32.97960.4521.6915.8184-2.34642.19650.1681-0.4977-0.42240.2366-0.237-0.66630.0293-0.03690.06890.0450.0686-0.02920.57750.17030.1369103.2341113.9036152.6684
41.6428-0.1822-1.41843.27221.8022.6056-0.0527-0.7237-0.16530.08480.0173-0.09890.09190.52860.03540.09960.0544-0.05450.46430.09330.0665101.5222118.5096144.7921
57.7172-3.4555-5.05551.79042.81684.6375-0.0203-0.62290.2507-0.08310.1712-0.1087-0.18380.2672-0.15090.1536-0.0396-0.01770.3304-0.02190.0994104.5293132.5613143.5191
62.1020.3985-0.42091.3020.05141.751-0.0599-0.3299-0.0839-0.2294-0.01960.1683-0.02480.13080.07950.13110.0302-0.05710.19060.02970.042193.0358122.0074133.676
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 17
2X-RAY DIFFRACTION2A18 - 48
3X-RAY DIFFRACTION3A49 - 71
4X-RAY DIFFRACTION4A72 - 105
5X-RAY DIFFRACTION5A106 - 119
6X-RAY DIFFRACTION6A120 - 323

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