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- PDB-2a2m: CRYSTAL STRUCTURE OF a putativeTenA family transcriptional regula... -

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Basic information

Entry
Database: PDB / ID: 2a2m
TitleCRYSTAL STRUCTURE OF a putativeTenA family transcriptional regulator (BT_3146) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 1.88 A RESOLUTION
Componentshypothetical protein BT3146
KeywordsTRANSCRIPTION / PUTATIVE TENA FAMILY TRANSCRIPTIONAL REGULATOR / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homologyHeme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha / cytosol / ACETATE ION / TenA family transcriptional activator-like protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.88 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of (np_812058.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.88 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 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 1.3Jan 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
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein BT3146
B: hypothetical protein BT3146
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,05519
Polymers60,0152
Non-polymers1,04017
Water10,989610
1
A: hypothetical protein BT3146
B: hypothetical protein BT3146
hetero molecules

A: hypothetical protein BT3146
B: hypothetical protein BT3146
hetero molecules

A: hypothetical protein BT3146
B: hypothetical protein BT3146
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,16457
Polymers180,0446
Non-polymers3,12051
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation33_545y,z-1/2,x+1/21
crystal symmetry operation53_455z-1/2,x,y+1/21
Buried area13730 Å2
ΔGint-82 kcal/mol
Surface area51160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)283.292, 283.292, 283.292
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number209
Space group name H-MF432
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 4

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGCYSAA12 - 9624 - 108
21ARGCYSBB12 - 9624 - 108
32ASPTHRAA99 - 237111 - 249
42ASPTHRBB99 - 237111 - 249

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Components

#1: Protein hypothetical protein BT3146


Mass: 30007.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: np_812058.1 / Plasmid: HK100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A309
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / 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: 3.77 Å3/Da / Density % sol: 67.11 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5
Details: 1.0M LiCl, 10.0% PEG-6000, 0.1M Citrate pH 5.0 VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 6, 2005 / Details: Flat mirror, double crystal monochromator, toroid
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.88→164.4 Å / Num. all: 74704 / Num. obs: 70979 / % possible obs: 91.5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.74
Reflection shell

Rmerge(I) obs: 0.819 / Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)% possible obs (%)Mean I/σ(I) obsNum. measured obsNum. unique obs
1.88-1.9560.82.04382489433
1.95-2.0374.32.745157211328
2.03-2.1290.24.067048713040
2.12-2.2397.15.99104714233
2.23-2.3798.17.959370014618
2.37-2.5598.510.749322814502
2.55-2.8199.114.599640414977
2.81-3.2199.519.449428614667
3.21-4.0499.827.369513214949
4.0498.933.899259814948

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.601data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.88→164.4 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / SU B: 3.433 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.081
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. POOR DENSITIES: THE DENSITY FOR 239 AND 240 ARE POOR. THE DENSITY IS AMBIGUOUS AT ARG 10 IN BOTH A AND B CHAINS, AS A RESULT, THE MODEL BUILT FOR THIS RESIDUE IS LESS RELIABLE. 4. A CHAIN OF DENSITY NEAR DIMER-DIMER INTERFACE (NEAR B178) IS TENATIVELY MODELLED AS A WATER CHAIN (151,167,171,205,223).
RfactorNum. reflection% reflectionSelection details
Rfree0.165 3725 5 %RANDOM
Rwork0.142 ---
all0.143 74704 --
obs-70979 94.58 %-
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: 26.381 Å2
Refinement stepCycle: LAST / Resolution: 1.88→164.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3702 0 68 610 4380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223989
X-RAY DIFFRACTIONr_bond_other_d0.0030.023448
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.9445445
X-RAY DIFFRACTIONr_angle_other_deg0.8438027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8345505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.9924.242198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9215613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8281520
X-RAY DIFFRACTIONr_chiral_restr0.0810.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024534
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02868
X-RAY DIFFRACTIONr_nbd_refined0.2250.2935
X-RAY DIFFRACTIONr_nbd_other0.1810.23401
X-RAY DIFFRACTIONr_nbtor_refined0.1930.22067
X-RAY DIFFRACTIONr_nbtor_other0.0860.22028
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2437
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0820.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.221
X-RAY DIFFRACTIONr_mcbond_it1.83632432
X-RAY DIFFRACTIONr_mcbond_other0.563964
X-RAY DIFFRACTIONr_mcangle_it2.83953841
X-RAY DIFFRACTIONr_scbond_it4.67681843
X-RAY DIFFRACTIONr_scangle_it6.29111580
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3398 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.260.5
medium thermal0.752
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 181 -
Rwork0.231 3777 -
obs--68.61 %
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)
10.5305-0.3048-0.2290.52470.06960.6420.0318-0.0052-0.02230.021-0.0304-0.01150.0464-0.0202-0.0014-0.04640.0138-0.0001-0.0170.0269-0.0238117.36166.739235.988
20.6501-0.254-0.18550.4295-0.09220.403-0.011-0.07510.04430.0198-0.0016-0.039-0.05530.06210.0125-0.04360.00140.013-0.0060.0166-0.0056125.98899.737217.265
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 24022 - 252
2X-RAY DIFFRACTION2BB10 - 24022 - 252

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