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- PDB-1ybx: Conserved hypothetical protein Cth-383 from Clostridium thermocellum -

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Basic information

Entry
Database: PDB / ID: 1ybx
TitleConserved hypothetical protein Cth-383 from Clostridium thermocellum
ComponentsConserved hypothetical protein
Keywordsstructural genomics / unknown function / conserved hypothetical protein / Clostridium thermocellum / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


bacterial nucleoid / DNA binding / cytoplasm
Similarity search - Function
Nucleoid-associated protein YbaB-like domain / Nucleoid-associated protein YbaB/EbfC family / YbaB/EbfC DNA-binding family / Ybab; Chain: A; / Nucleoid-associated protein YbaB-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Nucleoid-associated protein Cthe_2143
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAS / SAD / Resolution: 1.8 Å
AuthorsTempel, W. / Chang, J. / Zhao, M. / Habel, J. / Kataeva, I. / Xu, H. / Chen, L. / Lee, D. / Nguyen, J. / Chang, S.-H. ...Tempel, W. / Chang, J. / Zhao, M. / Habel, J. / Kataeva, I. / Xu, H. / Chen, L. / Lee, D. / Nguyen, J. / Chang, S.-H. / Horanyi, P. / Florence, Q. / Zhou, W. / Lin, D. / Zhang, H. / Ljundahl, L. / Liu, Z.-J. / Rose, J. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be published
Title: Conserved hypothetical protein Cth-383 from Clostridium thermocellum
Authors: Tempel, W. / Chang, J. / Zhao, M. / Habel, J. / Kataeva, I. / Xu, H. / Chen, L. / Lee, D. / Nguyen, J. / Chang, S.-H. / Horanyi, P. / Florence, Q. / Zhou, W. / Lin, D. / Zhang, H. / ...Authors: Tempel, W. / Chang, J. / Zhao, M. / Habel, J. / Kataeva, I. / Xu, H. / Chen, L. / Lee, D. / Nguyen, J. / Chang, S.-H. / Horanyi, P. / Florence, Q. / Zhou, W. / Lin, D. / Zhang, H. / Ljundahl, L. / Liu, Z.-J. / Rose, J. / Wang, B.-C.
History
DepositionDec 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 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
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved hypothetical protein
B: Conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)31,0086
Polymers31,0082
Non-polymers04
Water1,62190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-14 kcal/mol
Surface area10410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.914, 36.792, 61.824
Angle α, β, γ (deg.)90.00, 111.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Conserved hypothetical protein


Mass: 15503.752 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 48857448, UniProt: A3DHB8*PLUS
#2: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 90 / 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 % sol: 27.57 %
Crystal growTemperature: 291 K / Method: modified microbatch
Details: 20% w/v PEG 3350, 0.2M trilithium citrate, modified microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.71→50 Å / Num. obs: 16740 / % possible obs: 73.3 % / Rmerge(I) obs: 0.063 / Χ2: 1.567
Reflection shell
Resolution (Å)Rmerge(I) obsNum. measured allΧ2Diffraction-ID% possible all
1.71-1.770.3962741.148112.1
1.77-1.840.345380.963123.9
1.84-1.930.2539810.951143.1
1.93-2.030.21614971.075167.2
2.03-2.150.1820021.064187.1
2.15-2.320.13922131.171198
2.32-2.550.10322651.261199.9
2.55-2.920.07122911.3631100
2.92-3.680.05123122.0351100
3.68-500.04723672.688199.8

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.2 Å / D res low: 20 Å / FOM : 0.31 / Reflection: 10520
Phasing MAD shell
Resolution (Å)FOM Reflection
7.62-200.36559
4.91-7.620.4910
3.87-4.910.41125
3.3-3.870.391320
2.92-3.30.361488
2.64-2.920.31630
2.44-2.640.231729
2.27-2.440.161759
Phasing dmFOM : 0.59 / FOM acentric: 0.58 / FOM centric: 0.68 / Reflection: 13702 / Reflection acentric: 12596 / Reflection centric: 1106
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-19.5950.920.920.79638513125
3.6-5.70.910.920.8719331722211
2.9-3.60.80.80.8124182212206
2.5-2.90.630.630.7424182255163
2.1-2.50.440.430.5941933932261
2-2.10.20.20.2321021962140

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1data extraction
MAR345data collection
ISASphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAS / Resolution: 1.8→30.964 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.26 / WRfactor Rwork: 0.224 / SU B: 7.572 / SU ML: 0.116 / SU R Cruickshank DPI: 0.159 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.143 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2564 840 5.164 %thin shells
Rwork0.2246 ---
all0.226 ---
obs0.22621 16267 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 28.263 Å2
Baniso -1Baniso -2Baniso -3
1--0.354 Å20 Å2-0.413 Å2
2--1.125 Å20 Å2
3----1.079 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1337 0 4 90 1431
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221348
X-RAY DIFFRACTIONr_bond_other_d0.0010.021320
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9891821
X-RAY DIFFRACTIONr_angle_other_deg0.84233058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7465183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55227.55149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50615263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.756156
X-RAY DIFFRACTIONr_chiral_restr0.090.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021487
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02203
X-RAY DIFFRACTIONr_nbd_refined0.210.2260
X-RAY DIFFRACTIONr_nbd_other0.1650.21184
X-RAY DIFFRACTIONr_nbtor_refined0.1520.2663
X-RAY DIFFRACTIONr_nbtor_other0.0820.2828
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2720.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.29
X-RAY DIFFRACTIONr_mcbond_it1.2991.5964
X-RAY DIFFRACTIONr_mcbond_other0.2951.5376
X-RAY DIFFRACTIONr_mcangle_it1.45921476
X-RAY DIFFRACTIONr_mcangle_other0.63821255
X-RAY DIFFRACTIONr_scbond_it3.1643438
X-RAY DIFFRACTIONr_scbond_other0.6453956
X-RAY DIFFRACTIONr_scangle_it5.0314.5345
X-RAY DIFFRACTIONr_scangle_other1.8784.51803
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.84700.341387387
1.847-1.8970.337350.294542577
1.897-1.9520.467350.266699734
1.952-2.0120.239700.243827897
2.012-2.0780.309350.259911026
2.078-2.150.288700.22610531123
2.15-2.2310.277660.22610951161
2.231-2.3210.261390.21411001139
2.321-2.4240.246700.22610331103
2.424-2.5420.303350.22110141049
2.542-2.6780.266700.2229411011
2.678-2.8390.331350.237930965
2.839-3.0330.26700.236847917
3.033-3.2740.233350.232802837
3.274-3.5820.248350.217745780
3.582-3.9980.266350.199667702
3.998-4.6040.166350.167596631
4.604-5.6080.236350.212504539
5.608-7.8040.277350.282388423
7.804-30.96400.264266266
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)
12.0108-0.7285-2.34841.31362.90667.10430.0225-0.26220.0942-0.01940.04830.0247-0.18620.3435-0.0708-0.03940.0157-0.00850.02080.0213-0.1602-12.65713.52855.701
22.0375-0.40851.69521.0346-1.8225.06120.0625-0.2283-0.23890.09280.023-0.08880.16630.0183-0.0855-0.04430.0095-0.0372-0.0001-0.0135-0.1435-8.469-2.63456.155
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA13 - 10343 - 133
22BB12 - 10342 - 133

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