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- PDB-1zyb: Crystal structure of transcription regulator from Bacteroides the... -

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Basic information

Entry
Database: PDB / ID: 1zyb
TitleCrystal structure of transcription regulator from Bacteroides thetaiotaomicron VPI-5482 at 2.15 A resolution
Componentstranscription regulator, CRP family
KeywordsTRANSCRIPTION REGULATOR / np_813211.1 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / Winged helix DNA-binding domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Transcription regulator, CRP family
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of transcription regulator from Bacteroides thetaiotaomicron VPI-5482 at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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

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Assembly

Deposited unit
A: transcription regulator, CRP family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8548
Polymers27,2101
Non-polymers6457
Water3,369187
1
A: transcription regulator, CRP family
hetero molecules

A: transcription regulator, CRP family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,70816
Polymers54,4192
Non-polymers1,28914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area7830 Å2
ΔGint-42 kcal/mol
Surface area22000 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)115.980, 115.980, 119.639
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-339-

HOH

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Components

#1: Protein transcription regulator, CRP family


Mass: 27209.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: np_813211.1 / Production host: Escherichia coli (E. coli) / References: GenBank: 29349708, UniProt: Q89ZS6*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 3.86 Å3/Da / Density % sol: 67.86 %
Crystal growTemperature: 273 K
Details: 4.0M NaFormate, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.979094, 0.918381
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2005 / Details: Double-crystal monochromator (Si 111), toroid
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9790941
20.9183811
ReflectionResolution: 2.1→29.91 Å / Num. obs: 28282 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.1-2.1598.84.20.766120270.766
2.15-2.2110050.6491.219860.649
2.21-2.281006.30.6171.219510.617
2.28-2.351007.40.5171.519040.517
2.35-2.421007.30.4041.918230.404
2.42-2.511007.30.3152.417970.315
2.51-2.61007.30.2632.917240.263
2.6-2.711007.30.2043.716420.204
2.71-2.831007.30.1624.716030.162
2.83-2.971007.30.1236.115310.123
2.97-3.131007.20.0997.214670.099
3.13-3.321007.20.0857.913800.085
3.32-3.551007.20.0738.913110.073
3.55-3.831007.10.0649.412200.064
3.83-4.21007.10.05810.611330.058
4.2-4.710070.05211.210380.052
4.7-5.421006.90.04912.29360.049
5.42-6.641006.80.05210.37970.052
6.64-9.3999.86.40.03714.46370.037
9.39-29.91965.60.03216.33750.032

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→29.2 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.237 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.146
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.7 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. THERE EXISTS A PARTIAL DISULFIDE BOND BETWEEN CYS 53 AND CYS 109.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1332 5 %RANDOM
Rwork0.177 ---
all0.18 ---
obs-25047 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.566 Å2
Baniso -1Baniso -2Baniso -3
1--1.33 Å2-0.66 Å20 Å2
2---1.33 Å20 Å2
3---1.99 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1863 0 42 187 2092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222000
X-RAY DIFFRACTIONr_bond_other_d0.0010.021825
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9662700
X-RAY DIFFRACTIONr_angle_other_deg0.78134272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.565229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44424.79698
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98715369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.613158
X-RAY DIFFRACTIONr_chiral_restr0.0840.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022116
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02379
X-RAY DIFFRACTIONr_nbd_refined0.210.2377
X-RAY DIFFRACTIONr_nbd_other0.1730.21741
X-RAY DIFFRACTIONr_nbtor_refined0.1810.2945
X-RAY DIFFRACTIONr_nbtor_other0.0850.21223
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2142
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.240.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.215
X-RAY DIFFRACTIONr_mcbond_it2.39531262
X-RAY DIFFRACTIONr_mcbond_other0.5293462
X-RAY DIFFRACTIONr_mcangle_it3.22651914
X-RAY DIFFRACTIONr_scbond_it5.6048897
X-RAY DIFFRACTIONr_scangle_it7.47411786
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 97 -
Rwork0.229 1808 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -23.4662 Å / Origin y: 43.993 Å / Origin z: 1.7133 Å
111213212223313233
T-0.1211 Å2-0.0239 Å2-0.0332 Å2-0.0545 Å20.1586 Å2---0.0891 Å2
L1.3136 °20.9782 °2-0.5254 °2-1.6663 °2-0.1776 °2--0.2588 °2
S-0.0555 Å °-0.2061 Å °-0.0828 Å °0.1045 Å °0.0442 Å °0.0182 Å °-0.0197 Å °0.1377 Å °0.0114 Å °

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