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- PDB-3nze: The crystal structure of a domain of a possible sugar-binding tra... -

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Basic information

Entry
Database: PDB / ID: 3nze
TitleThe crystal structure of a domain of a possible sugar-binding transcriptional regulator from Arthrobacter aurescens TC1.
ComponentsPutative transcriptional regulator, sugar-binding family
KeywordsTranscription regulator / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


carbohydrate binding / DNA binding / metal ion binding
Similarity search - Function
Sugar-binding domain, putative / : / Putative sugar-binding domain / Rossmann fold - #1360 / NagB/RpiA transferase-like / Homeobox-like domain superfamily / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative transcriptional regulator, sugar-binding family
Similarity search - Component
Biological speciesArthrobacter aurescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.697 Å
AuthorsTan, K. / Zhang, R. / Bigelow, L. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a domain of a possible sugar-binding transcriptional regulator from Arthrobacter aurescens TC1.
Authors: Tan, K. / Zhang, R. / Bigelow, L. / Buck, K. / Joachimiak, A.
History
DepositionJul 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_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_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Putative transcriptional regulator, sugar-binding family
B: Putative transcriptional regulator, sugar-binding family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2094
Polymers58,1292
Non-polymers802
Water7,116395
1
A: Putative transcriptional regulator, sugar-binding family


Theoretical massNumber of molelcules
Total (without water)29,0641
Polymers29,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative transcriptional regulator, sugar-binding family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1453
Polymers29,0641
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Putative transcriptional regulator, sugar-binding family
hetero molecules

A: Putative transcriptional regulator, sugar-binding family


Theoretical massNumber of molelcules
Total (without water)58,2094
Polymers58,1292
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area2730 Å2
ΔGint-25 kcal/mol
Surface area21320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.337, 86.286, 64.641
Angle α, β, γ (deg.)90.00, 94.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative transcriptional regulator, sugar-binding family


Mass: 29064.391 Da / Num. of mol.: 2 / Fragment: sequence database residues 56-319
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter aurescens (bacteria) / Strain: TC1 / Gene: AAur_2250 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: A1R6X9
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 1.97 Å3/Da / Density % sol: 37.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10% 2-propanol, 0.1M MES, 0.2M calcium acetate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 16, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.7→36 Å / Num. all: 49143 / Num. obs: 49143 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 19.46 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 14.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 2 / Num. unique all: 2138 / % possible all: 84.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.697→36 Å / SU ML: 0.18 / σ(F): 0.03 / Phase error: 20.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1991 2405 5.05 %random
Rwork0.1682 ---
obs0.1698 47627 95.3 %-
all-47627 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.035 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.3626 Å20 Å20.1774 Å2
2--6.7041 Å20 Å2
3----3.3415 Å2
Refinement stepCycle: LAST / Resolution: 1.697→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3912 0 2 395 4309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064057
X-RAY DIFFRACTIONf_angle_d1.0265528
X-RAY DIFFRACTIONf_dihedral_angle_d17.1511470
X-RAY DIFFRACTIONf_chiral_restr0.072647
X-RAY DIFFRACTIONf_plane_restr0.004730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6969-1.75750.28431980.21183960X-RAY DIFFRACTION83
1.7575-1.82790.22492220.17914397X-RAY DIFFRACTION93
1.8279-1.9110.21692470.17124446X-RAY DIFFRACTION95
1.911-2.01180.22132330.17854614X-RAY DIFFRACTION97
2.0118-2.13780.22022420.16794663X-RAY DIFFRACTION98
2.1378-2.30290.21462530.16684669X-RAY DIFFRACTION98
2.3029-2.53460.21472590.16814668X-RAY DIFFRACTION99
2.5346-2.90120.20772600.1754720X-RAY DIFFRACTION100
2.9012-3.65460.19312540.16234673X-RAY DIFFRACTION98
3.6546-36.09680.16082370.15564412X-RAY DIFFRACTION91
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)
10.65450.1995-0.57070.5875-0.3411.5221-0.02460.0822-0.08220.0708-0.0243-0.01540.00450.038-00.1365-0.0252-0.01950.1632-0.01010.13544.173337.657233.6834
20.859-0.1540.21180.8325-0.63161.28990.0259-0.04150.0679-0.0155-0.0624-0.0361-0.05050.024600.11630.00010.01420.086-0.01320.13352.630453.654964.118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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