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- PDB-2a6c: CRYSTAL STRUCTURE OF A PUTATIVE TRANSCRIPTIONAL REGULATOR (NE_135... -

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Basic information

Entry
Database: PDB / ID: 2a6c
TitleCRYSTAL STRUCTURE OF A PUTATIVE TRANSCRIPTIONAL REGULATOR (NE_1354) FROM NITROSOMONAS EUROPAEA AT 1.90 A RESOLUTION
ComponentsHelix-turn-helix motif
KeywordsTRANSCRIPTION / PUTATIVE TRANSCRIPTIONAL REGULATOR / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


HigA2-like, helix-turn-helix domain / Helix-turn-helix domain / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / Helix-turn-helix motif
Similarity search - Component
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of (np_841403.1) from NITROSOMONAS EUROPAEA at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 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
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Helix-turn-helix motif
B: Helix-turn-helix motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7296
Polymers19,2912
Non-polymers4384
Water1,29772
1
A: Helix-turn-helix motif
hetero molecules

A: Helix-turn-helix motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4154
Polymers19,2912
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2470 Å2
ΔGint-14 kcal/mol
Surface area8180 Å2
MethodPISA, PQS
2
B: Helix-turn-helix motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0224
Polymers9,6461
Non-polymers3763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Helix-turn-helix motif
hetero molecules

B: Helix-turn-helix motif
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0448
Polymers19,2912
Non-polymers7536
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)87.862, 40.788, 53.393
Angle α, β, γ (deg.)90.000, 119.830, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-102-

HOH

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Components

#1: Protein Helix-turn-helix motif


Mass: 9645.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Gene: np_841403.1 / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q82UW4
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.3 Å3/Da / Density % sol: 46.01 %
Crystal growTemperature: 273 K / pH: 4.2
Details: 40.0 % MPD, 0.1M Phosphate Citrate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K, pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97929, 0.91162
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 2, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.911621
ReflectionResolution: 1.8→26.48 Å / Num. obs: 14998 / % possible obs: 97.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.095 / Rsym value: 0.095 / Net I/σ(I): 3.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
1.8-1.8584.53.30.5161.29540.516
1.85-1.997.13.70.4551.510450.455
1.9-1.9598.53.80.3771.710560.377
1.95-2.0198.23.80.308210120.308
2.01-2.0898.53.80.2612.610040.261
2.08-2.1598.33.80.20839590.208
2.15-2.23993.80.173.79350.17
2.23-2.3298.93.80.1464.29010.146
2.32-2.4398.63.80.1354.68590.135
2.43-2.55993.80.12458270.124
2.55-2.6899.23.80.1035.77760.103
2.68-2.8599.53.70.0956.27470.095
2.85-3.0499.33.70.0877.26870.087
3.04-3.2999.53.70.0816.96570.081
3.29-3.699.53.70.0737.36150.073
3.6-4.0299.63.70.06295500.062
4.02-4.6599.53.70.0716.54820.071
4.65-5.6999.53.60.07454170.074
5.69-8.0599.73.40.0715.93300.071
8.05-26.4897.43.20.0687.41850.068

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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: 1.9→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.221 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.152
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.241 672 5.2 %RANDOM
Rwork0.182 ---
all0.185 ---
obs-12269 98.61 %-
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: 28.913 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20.83 Å2
2--2.85 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1178 0 29 72 1279
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211234
X-RAY DIFFRACTIONr_bond_other_d0.0010.021186
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9721659
X-RAY DIFFRACTIONr_angle_other_deg0.84432733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0355154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.37923.12548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.33515230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.684158
X-RAY DIFFRACTIONr_chiral_restr0.0870.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021330
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02230
X-RAY DIFFRACTIONr_nbd_refined0.2150.2249
X-RAY DIFFRACTIONr_nbd_other0.1730.21137
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2602
X-RAY DIFFRACTIONr_nbtor_other0.0810.2778
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.246
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.29
X-RAY DIFFRACTIONr_mcbond_it2.3473791
X-RAY DIFFRACTIONr_mcbond_other0.6513318
X-RAY DIFFRACTIONr_mcangle_it2.86151231
X-RAY DIFFRACTIONr_scbond_it5.4528475
X-RAY DIFFRACTIONr_scangle_it7.44211428
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 52 -
Rwork0.21 899 -
obs--98.14 %

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