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- PDB-2a2o: CRYSTAL STRUCTURE OF a putativeTenA family transcriptional regula... -

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Entry
Database: PDB / ID: 2a2o
TitleCRYSTAL STRUCTURE OF a putativeTenA family transcriptional regulator (BT_3146) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.16 A RESOLUTION
Componentshypothetical protein BT3146
KeywordsTRANSCRIPTION / PUTATIVE TENA FAMILY TRANSCRIPTIONAL REGULATOR / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology: / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha / cytosol / : / TenA family transcriptional activator-like protein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.16 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of (np_812058.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.16 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr1_auth_asym_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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 7 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 7 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

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein BT3146
B: hypothetical protein BT3146
C: hypothetical protein BT3146
D: hypothetical protein BT3146
E: hypothetical protein BT3146
F: hypothetical protein BT3146
G: hypothetical protein BT3146
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,10243
Polymers210,0517
Non-polymers2,05136
Water30,8961715
1
A: hypothetical protein BT3146
B: hypothetical protein BT3146
C: hypothetical protein BT3146
D: hypothetical protein BT3146
E: hypothetical protein BT3146
F: hypothetical protein BT3146
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,80737
Polymers180,0446
Non-polymers1,76331
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16730 Å2
ΔGint10 kcal/mol
Surface area50200 Å2
MethodPISA
2
G: hypothetical protein BT3146
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)181,76836
Polymers180,0446
Non-polymers1,72430
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-y+2,x-y+1,z1
crystal symmetry operation3_675-x+y+1,-x+2,z1
crystal symmetry operation10_775-y+2,-x+2,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Unit cell
Length a, b, c (Å)201.238, 201.238, 291.030
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11G-247-

K

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81A
91B
101C
111D
121E
131F
141G

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSALAALAAA11 - 9423 - 106
21LYSLYSALAALABB11 - 9423 - 106
31LYSLYSALAALACC11 - 9423 - 106
41LYSLYSALAALADD11 - 9423 - 106
51LYSLYSALAALAEE11 - 9423 - 106
61LYSLYSALAALAFF11 - 9423 - 106
71LYSLYSALAALAGG11 - 9423 - 106
82THRTHRLEULEUAA101 - 239113 - 251
92THRTHRLEULEUBB101 - 239113 - 251
102THRTHRLEULEUCC101 - 239113 - 251
112THRTHRLEULEUDD101 - 239113 - 251
122THRTHRLEULEUEE101 - 239113 - 251
132THRTHRLEULEUFF101 - 239113 - 251
142THRTHRLEULEUGG101 - 239113 - 251
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.

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Components

#1: Protein
hypothetical protein BT3146


Mass: 30007.312 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: np_812058.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8A309
#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1715 / 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: 4.08 Å3/Da / Density % sol: 69.64 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5
Details: 1.0M LiCl, 10.0% PEG-6000, 0.1M Citrate pH5.0 , 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 / Wavelength: 0.97934, 0.89194
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 12, 2005 / Details: Flat mirror, double crystal monochromator, toroid
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.891941
ReflectionResolution: 2.16→48.85 Å / Num. obs: 175804 / % possible obs: 95.6 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.16-2.2890.240.431.8238000.43
2.28-2.41945.70.3482.2235840.348
2.41-2.5896.18.10.2922.6228080.292
2.58-2.7996.58.30.2143.5213050.214
2.79-3.0596.98.30.1564.8197530.156
3.05-3.4297.28.30.1086.7179920.108
3.42-3.9497.78.20.0719.9160610.071
3.94-4.83988.10.06210.7136700.062
4.83-6.83987.90.05911.3107260.059
6.83-48.8596.87.40.03616.861060.036

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
XDSdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.16→48.85 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 5.535 / SU ML: 0.075 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.115
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. POORLY DEFINED RESIDUES: A/B/C/E/G10, E/F191, THE MODELS FOR THESE RESIDUES MAY BE NOT VERY RELIABLE. 3. THE OLIGOMERIC STATE IS ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. POORLY DEFINED RESIDUES: A/B/C/E/G10, E/F191, THE MODELS FOR THESE RESIDUES MAY BE NOT VERY RELIABLE. 3. THE OLIGOMERIC STATE IS ASSIGNED AS HEXAMER CONSISTING OF THREE LOOSELY ASSOCIATED DIMERS. THIS IS SUPPORTED BY SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING. 4. POTASSIUM IONS ARE TENTATIVELY ASSIGNED TO INTERPRET THE DENSITY WHICH CANNOT BE EXPLAINED BY WATERS. 5. 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. 6. LOOPS 97-99 ADOPTS DIFFERENT CONFORMATIONS BETWEEN CHAIN A/C/F AND B/D/E/G.
RfactorNum. reflection% reflectionSelection details
Rfree0.173 8818 5 %RANDOM
Rwork0.145 ---
all0.146 ---
obs-166931 95.27 %-
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: 34.196 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.16→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12898 0 120 1715 14733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02213494
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211672
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.93918340
X-RAY DIFFRACTIONr_angle_other_deg0.917327110
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.81451601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80824.134670
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.589152093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4671567
X-RAY DIFFRACTIONr_chiral_restr0.0860.21952
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215053
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022933
X-RAY DIFFRACTIONr_nbd_refined0.2260.23149
X-RAY DIFFRACTIONr_nbd_other0.1790.211578
X-RAY DIFFRACTIONr_nbtor_refined0.1950.26957
X-RAY DIFFRACTIONr_nbtor_other0.0880.26859
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.21158
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.2101
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.223
X-RAY DIFFRACTIONr_mcbond_it1.38838030
X-RAY DIFFRACTIONr_mcbond_other0.25933272
X-RAY DIFFRACTIONr_mcangle_it2.837512943
X-RAY DIFFRACTIONr_scbond_it5.0985590
X-RAY DIFFRACTIONr_scangle_it7.472115397
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1313TIGHT POSITIONAL0.050.05
2B1313TIGHT POSITIONAL0.040.05
3C1313TIGHT POSITIONAL0.060.05
4D1313TIGHT POSITIONAL0.050.05
5E1313TIGHT POSITIONAL0.060.05
6F1313TIGHT POSITIONAL0.070.05
7G1313TIGHT POSITIONAL0.040.05
1A1949MEDIUM POSITIONAL0.280.5
2B1949MEDIUM POSITIONAL0.220.5
3C1949MEDIUM POSITIONAL0.250.5
4D1949MEDIUM POSITIONAL0.290.5
5E1949MEDIUM POSITIONAL0.310.5
6F1949MEDIUM POSITIONAL0.30.5
7G1949MEDIUM POSITIONAL0.230.5
1A1313TIGHT THERMAL0.170.5
2B1313TIGHT THERMAL0.170.5
3C1313TIGHT THERMAL0.190.5
4D1313TIGHT THERMAL0.180.5
5E1313TIGHT THERMAL0.180.5
6F1313TIGHT THERMAL0.180.5
7G1313TIGHT THERMAL0.170.5
1A1949MEDIUM THERMAL0.782
2B1949MEDIUM THERMAL0.812
3C1949MEDIUM THERMAL0.872
4D1949MEDIUM THERMAL0.862
5E1949MEDIUM THERMAL0.922
6F1949MEDIUM THERMAL0.912
7G1949MEDIUM THERMAL0.842
LS refinement shellResolution: 2.16→2.216 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 639 -
Rwork0.217 11269 -
obs--88.52 %
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)
10.81190.29870.63030.6989-0.16471.4129-0.0536-0.10630.11110.05710.01090.0751-0.0941-0.14330.0427-0.02580.0052-0.0263-0.04530.0041-0.026950.223222.74755.21
20.84620.14030.58020.5809-0.08411.52910.02150.0394-0.07410.0546-0.0073-0.04480.21210.0364-0.01420.0401-0.0312-0.0426-0.04230.0185-0.031942.133184.90349.915
30.73020.14180.06770.6793-0.10410.5521-0.0224-0.0438-0.0126-0.001-0.0192-0.0025-0.03070.01270.0416-0.0341-0.0118-0.0128-0.0642-0.0086-0.075412.263182.44427.325
40.4170.37960.15660.9585-0.12820.7722-0.00350.0519-0.0028-0.0282-0.0367-0.11450.05380.03320.0402-0.0195-0.00020.0107-0.05710.0048-0.056822.821197.265-7.316
50.4189-0.025-0.16070.7873-0.00550.35960.06060.047-0.0077-0.0303-0.06210.02050.002-0.00490.0015-0.0223-0.0272-0.007-0.05920.004-0.058630.697233.114-3.261
60.37330.2092-0.00810.5517-0.35230.718-0.0003-0.0095-0.0466-0.0154-0.0008-0.04960.06410.06120.0011-0.032-0.0167-0.0062-0.0320.009-0.047659.81237.32922.527
71.355-0.27820.19670.81660.17310.16530.00430.08210.057-0.08850.0091-0.0801-0.03440.0389-0.0134-0.0572-0.0060.0188-0.04810.0175-0.040483.14205.50965.927
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: all

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA10 - 23922 - 251
22BB10 - 23922 - 251
33CC10 - 23922 - 251
44DD11 - 23923 - 251
55EE10 - 23922 - 251
66FF11 - 23923 - 251
77GG10 - 23922 - 251

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