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- PDB-2a6b: Crystal structure of a putative transcriptional regulator of the ... -

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Basic information

Entry
Database: PDB / ID: 2a6b
TitleCrystal structure of a putative transcriptional regulator of the tena family (spr0628) from streptococcus pneumoniae r6 at 1.70 A resolution
Componentshypothetical protein spr0628
KeywordsTRANSCRIPTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


aminopyrimidine aminohydrolase / thiaminase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / cytosol
Similarity search - Function
TenA_E protein / : / Thiaminase-2/PQQC / TENA/THI-4/PQQC family / Heme oxygenase-like / Heme Oxygenase; Chain A / Haem oxygenase-like, multi-helical / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Aminopyrimidine aminohydrolase
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of (np_358222.1) from STREPTOCOCCUS PNEUMONIAE R6 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif
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
Revision 1.4Nov 6, 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

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Assembly

Deposited unit
A: hypothetical protein spr0628


Theoretical massNumber of molelcules
Total (without water)27,3381
Polymers27,3381
Non-polymers00
Water4,324240
1
A: hypothetical protein spr0628

A: hypothetical protein spr0628


Theoretical massNumber of molelcules
Total (without water)54,6762
Polymers54,6762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area1790 Å2
ΔGint-13 kcal/mol
Surface area18010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.908, 119.908, 47.105
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-224-

HOH

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Components

#1: Protein hypothetical protein spr0628


Mass: 27338.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Species: Streptococcus pneumoniae / Strain: ATCC BAA-255 / R6 / Gene: np_358222.1 / Plasmid: HK100 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8DQK6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
1358.65
2
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2731vapor diffusion, sitting drop, nanodropo.2M LiCl, 20.0% PEG-3350, No Buffer pH 6.7, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K
2732vapor diffusion, sitting drop, nanodrop0.2M NH4OAc, 30.0% PEG-4000, 0.1M Citrate pH 5.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 273K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-211
SYNCHROTRONSSRL BL1-520.918381, 0.978455, 0.978964, 1.033150
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDJun 1, 2005
ADSC QUANTUM 42CCDMay 5, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.9183811
30.9784551
40.9789641
51.033151
ReflectionResolution: 1.7→29.98 Å / Num. obs: 38398 / % possible obs: 100 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 4.4
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
1.7-1.741009.60.5131.328080.513
1.74-1.791009.60.4261.726980.426
1.79-1.841009.60.355226450.355
1.84-1.91009.60.2622.825770.262
1.9-1.961009.50.23325040.23
1.96-2.031009.60.1873.824290.187
2.03-2.111009.60.1474.723250.147
2.11-2.191009.60.1345.222410.134
2.19-2.291009.50.112621720.112
2.29-2.41009.50.0966.620860.096
2.4-2.531009.50.0926.919790.092
2.53-2.691009.40.0976.418840.097
2.69-2.871009.40.0946.417740.094
2.87-3.11009.40.0817.516520.081
3.1-3.41009.30.0738.315480.073
3.4-3.81009.20.0668.413840.066
3.8-4.391009.10.0638.212560.063
4.39-5.381008.80.0617.310760.061
5.38-7.61008.50.0578.28540.057
7.6-29.9898.17.30.0687.25060.068

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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: 1.7→29.98 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.776 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.071
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THERE MAY BE A MINOR DUAL CONFORMATION FROM RESIDUE 104 TO RESIDUE 116. THE SIDE CHAIN OF TYR110 CAN BE MODEL IN TWO ORIENTATION. IN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. THERE MAY BE A MINOR DUAL CONFORMATION FROM RESIDUE 104 TO RESIDUE 116. THE SIDE CHAIN OF TYR110 CAN BE MODEL IN TWO ORIENTATION. IN THIS MODEL ONLY ONE MODEL IS BUILT AND FIT IN THE DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.175 1937 5 %RANDOM
Rwork0.155 ---
all0.156 ---
obs-36426 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.293 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20 Å2
2---1.19 Å20 Å2
3---2.38 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 0 240 1998
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221826
X-RAY DIFFRACTIONr_bond_other_d0.0010.021620
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9372481
X-RAY DIFFRACTIONr_angle_other_deg1.27233753
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9335224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.21924.62493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86615298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.404156
X-RAY DIFFRACTIONr_chiral_restr0.0850.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022061
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02400
X-RAY DIFFRACTIONr_nbd_refined0.2250.2417
X-RAY DIFFRACTIONr_nbd_other0.1650.21576
X-RAY DIFFRACTIONr_nbtor_refined0.1920.2923
X-RAY DIFFRACTIONr_nbtor_other0.0840.21031
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2157
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0960.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1360.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.216
X-RAY DIFFRACTIONr_mcbond_it2.19231164
X-RAY DIFFRACTIONr_mcbond_other0.4673450
X-RAY DIFFRACTIONr_mcangle_it2.79751748
X-RAY DIFFRACTIONr_scbond_it4.7028826
X-RAY DIFFRACTIONr_scangle_it6.34911730
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 137 -
Rwork0.187 2665 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 21.1713 Å / Origin y: 44.5958 Å / Origin z: 23.1674 Å
111213212223313233
T-0.0501 Å20.0092 Å2-0.0148 Å2--0.0394 Å20.0185 Å2---0.0208 Å2
L0.6991 °20.0316 °2-0.0879 °2-1.0757 °20.1637 °2--0.5274 °2
S0.0041 Å °-0.0318 Å °0.0222 Å °0.0007 Å °0.0172 Å °0.0501 Å °-0.0116 Å °-0.0118 Å °-0.0213 Å °

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