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- PDB-4oqp: Structure of the effector-binding domain of deoxyribonucleoside r... -

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Basic information

Entry
Database: PDB / ID: 4oqp
TitleStructure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis in complex with deoxyribose-5-phosphate
ComponentsDeoxyribonucleoside regulator
KeywordsTRANSCRIPTION / Rossmann Fold / Sugar-binding transcriptional regulator / Schiff base
Function / homology
Function and homology information


regulation of DNA-templated transcription initiation / cis-regulatory region sequence-specific DNA binding / carbohydrate binding / identical protein binding
Similarity search - Function
Homeodomain-like domain / Sugar-binding domain, putative / : / Putative sugar-binding domain / Rossmann fold - #1360 / NagB/RpiA transferase-like / RNA polymerase sigma factor, region 3/4-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / : / NICKEL (II) ION / PENTANE-3,4-DIOL-5-PHOSPHATE / Deoxyribonucleoside regulator
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRezacova, P. / Skerlova, J.
Citation
Journal: Febs J. / Year: 2014
Title: Structure of the effector-binding domain of deoxyribonucleoside regulator DeoR from Bacillus subtilis.
Authors: Skerlova, J. / Fabry, M. / Hubalek, M. / Otwinowski, Z. / Rezacova, P.
#1: Journal: Mol.Microbiol. / Year: 2008
Title: Crystal structures of the effector-binding domain of repressor Central glycolytic gene Regulator from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates.
Authors: Rezacova, P. / Kozisek, M. / Moy, S.F. / Sieglova, I. / Joachimiak, A. / Machius, M. / Otwinowski, Z.
#2: Journal: Cryst.GrowthDes. / Year: 2013
Title: Crystallization of the Effector-Binding Domain of Repressor DeoR from Bacillus subtilis
Authors: Pisackova, J. / Prochazkova, K. / Fabry, M. / Rezacova, P.
History
DepositionFeb 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Deoxyribonucleoside regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9438
Polymers29,3711
Non-polymers5727
Water4,756264
1
A: Deoxyribonucleoside regulator
hetero molecules

A: Deoxyribonucleoside regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,88716
Polymers58,7432
Non-polymers1,14414
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area2960 Å2
ΔGint-75 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.995, 78.983, 91.338
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-503-

HOH

21A-607-

HOH

31A-612-

HOH

41A-632-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Deoxyribonucleoside regulator


Mass: 29371.447 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: deoR, yxxC, BSU39430 / Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39140

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Non-polymers , 6 types, 271 molecules

#2: Chemical ChemComp-PED / PENTANE-3,4-DIOL-5-PHOSPHATE / OPEN FORM OF 1'-2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE


Mass: 200.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H13O6P
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsTHE ORGINAL SUGAR D 2-DEOXYRIBOSE-5-PHOSPHATE WAS COVALENTLY BOUND TO LYS141 BY SCHIFF BASE. THE ...THE ORGINAL SUGAR D 2-DEOXYRIBOSE-5-PHOSPHATE WAS COVALENTLY BOUND TO LYS141 BY SCHIFF BASE. THE PRODUCT 3,4-DIHYDROXY-5-(PHOSPHONOOXY)PENTANE-LYS ADDUCT WAS OBTAINED. NZ LYS A 141 - C1' PED A 401 BOND REPRESENTS A DOUBLE BOND

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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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 291 K / pH: 7.5
Details: 0.08 M HEPES, 9.6% (w/v) PEG 3350, 4 mM CoCl2, 4 mM CdCl2, 4 mM MgCl2, and 4 mM NiCl2; 16.5 mg/mL protein in 20 mM trisodium citrate pH 7.0, 150 mM NaCl, 0.02% (v/v) 2-mercaptoethanol, 50 mM ...Details: 0.08 M HEPES, 9.6% (w/v) PEG 3350, 4 mM CoCl2, 4 mM CdCl2, 4 mM MgCl2, and 4 mM NiCl2; 16.5 mg/mL protein in 20 mM trisodium citrate pH 7.0, 150 mM NaCl, 0.02% (v/v) 2-mercaptoethanol, 50 mM deoxyribose-5-phosphate; protein:reservoir 2:1, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 17, 2012
Details: DOUBLE CRYSTAL MONOCHROMATOR WITH 2 SETS OF RH-SOATED SILLICON AND GLASS MIRRORS
RadiationMonochromator: SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 34660 / % possible obs: 93.5 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.04
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 2.8 / % possible all: 62.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NZE

3nze


Resolution: 1.6→19.77 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.784 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1750 5.1 %RANDOM
Rwork0.154 ---
obs0.156 32880 93.4 %-
all-37289 --
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: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1988 0 18 264 2270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192163
X-RAY DIFFRACTIONr_bond_other_d0.0020.022117
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9672949
X-RAY DIFFRACTIONr_angle_other_deg0.8473.0014894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7015294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75824.118102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84615403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4381516
X-RAY DIFFRACTIONr_chiral_restr0.130.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022480
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
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_it0.8381.0411057
X-RAY DIFFRACTIONr_mcbond_other0.8311.0391056
X-RAY DIFFRACTIONr_mcangle_it1.4351.5531330
X-RAY DIFFRACTIONr_mcangle_other1.4371.5551331
X-RAY DIFFRACTIONr_scbond_it1.0971.2251105
X-RAY DIFFRACTIONr_scbond_other1.0971.2251106
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7821.7821599
X-RAY DIFFRACTIONr_long_range_B_refined6.71510.3542678
X-RAY DIFFRACTIONr_long_range_B_other6.71410.3562679
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 74 -
Rwork0.237 1548 -
obs--59.99 %
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)
19.33322.69121.60523.0322-1.26554.23660.2016-1.02420.64220.4598-0.28960.0124-0.5676-0.07780.08790.1767-0.00950.01930.1317-0.08880.116715.42419.34234
25.8180.5126-1.32571.2432-1.68133.162-0.0139-0.3067-0.07370.2420.16910.3579-0.0924-0.4433-0.15510.115-0.02120.1550.1606-0.03490.21866.8937.92329.789
32.4996-1.43911.1988.5177-6.10665.98720.038-0.08110.0951-0.02250.10880.2741-0.0202-0.2763-0.14680.0138-0.0080.02250.14880.00180.14265.8739.35222.533
48.24536.7441-0.46118.38890.33216.05330.1825-0.04250.6197-0.1206-0.12390.7225-0.2501-0.2619-0.05860.10610.05780.0190.04010.01920.19638.80821.16715.378
50.5515-0.42560.29772.313-0.18461.62840.1020.16970.0017-0.087-0.01130.0424-0.0624-0.2398-0.09070.0720.04180.02860.140.01870.133115.30211.55711.432
62.2111.34591.09057.333-4.81618.2237-0.02280.09190.0710.07510.22170.39070.0378-0.5607-0.19890.02170.02130.00530.17910.02350.15215.03310.45712.853
70.8227-1.1601-0.26272.4463-0.01521.27110.06440.1545-0.093-0.0499-0.01980.1217-0.1429-0.0965-0.04450.08070.01460.00590.09460.02020.141416.837.876.353
82.8579-1.9254-1.02876.0102-2.19892.21590.14930.3641-0.1422-0.2941-0.08760.28750.0005-0.2903-0.06170.08410.0236-0.04040.19640.01280.099910.76510.1975.2
91.3832-0.8222-1.03441.1364-0.26742.2080.09920.1773-0.092-0.1216-0.090.0276-0.0604-0.0862-0.00920.1177-0.011-0.0210.0992-0.01390.108323.9845.3673.883
101.8983-3.15122.37948.8816-3.78627.17420.01250.08050.1955-0.0965-0.1199-0.2435-0.0670.41460.10730.0395-0.0195-0.00820.14520.00190.106136.5624.2772.812
112.5122-4.0158-2.89966.80875.28599.24140.13950.11620.0917-0.1277-0.04480.0437-0.37670.1331-0.09480.1382-0.03430.05320.09150.03670.158327.2116.0163.835
121.0866-0.2245-1.05320.77090.56891.39880.07720.01680.03120.16090.03020.1352-0.11940.0262-0.10740.1551-00.05360.05320.00120.171919.09310.0418.862
133.34120.15381.41880.29380.43211.8424-0.05210.0604-0.27340.0152-0.07730.04120.1521-0.22980.12930.1126-0.04620.02780.08-0.01260.139123.992-6.66217.849
146.1033-3.7654-5.6155.3111.746211.0406-0.19440.0256-0.14360.0262-0.11150.16290.18710.27380.30590.07920.0018-0.00350.04580.00390.137631.474-7.59421.81
153.4115-1.2962.16451.7549-0.53351.80040.0132-0.1669-0.00050.07880.12170.0323-0.0366-0.0127-0.1350.08480.0010.00480.1105-0.00390.098528.5363.08123.108
161.7066-1.4870.16241.6350.19051.4785-0.0406-0.03880.03710.0359-0.00110.0078-0.0510.24250.04180.0759-0.02150.00260.13170.00540.133.8515.30617.382
174.3763-0.3477-1.87583.49763.39397.98060.01-0.32460.05610.07820.05930.017-0.39430.5602-0.06920.1111-0.09540.02550.108-0.02250.128829.52716.67318.095
182.34393.2851-0.92565.0689-0.44656.03850.1716-0.02530.19120.0378-0.01830.474-0.5423-0.0155-0.15320.17290.027-0.00040.01230.01490.188418.91918.4218.927
195.14992.2535-0.76133.1878-1.26352.3882-0.0637-0.36540.15450.197-0.00410.0909-0.04780.00090.06780.08420.01520.01040.0833-0.02650.094421.7678.07228.526
202.72221.23-1.47670.8234-1.16564.8894-0.0187-0.4940.28970.0772-0.04240.1187-0.2192-0.15960.06110.10160.05130.03210.2069-0.06390.109314.52611.96532.395
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A58 - 76
2X-RAY DIFFRACTION2A77 - 88
3X-RAY DIFFRACTION3A89 - 99
4X-RAY DIFFRACTION4A100 - 107
5X-RAY DIFFRACTION5A108 - 121
6X-RAY DIFFRACTION6A122 - 129
7X-RAY DIFFRACTION7A130 - 151
8X-RAY DIFFRACTION8A152 - 167
9X-RAY DIFFRACTION9A168 - 177
10X-RAY DIFFRACTION10A178 - 190
11X-RAY DIFFRACTION11A191 - 203
12X-RAY DIFFRACTION12A204 - 211
13X-RAY DIFFRACTION13A212 - 226
14X-RAY DIFFRACTION14A227 - 233
15X-RAY DIFFRACTION15A234 - 247
16X-RAY DIFFRACTION16A248 - 264
17X-RAY DIFFRACTION17A265 - 270
18X-RAY DIFFRACTION18A271 - 277
19X-RAY DIFFRACTION19A278 - 295
20X-RAY DIFFRACTION20A296 - 311

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