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- PDB-4n6c: Crystal Structure of the B1RZQ2 protein from Streptococcus pneumo... -

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Basic information

Entry
Database: PDB / ID: 4n6c
TitleCrystal Structure of the B1RZQ2 protein from Streptococcus pneumoniae. Northeast Structural Genomics Consortium (NESG) Target SpR36.
Componentsuncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / SpR36 / PF08020 / DUF1706
Function / homologydinb family like domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / BROMIDE ION / :
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.548 Å
AuthorsVorobiev, S. / Seetharaman, J. / Patel, D. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. ...Vorobiev, S. / Seetharaman, J. / Patel, D. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the B1RZQ2 protein from Streptococcus pneumoniae.
Authors: Vorobiev, S. / Seetharaman, J. / Patel, D. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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_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: uncharacterized protein
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4114
Polymers44,2512
Non-polymers1602
Water5,314295
1
A: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2052
Polymers22,1251
Non-polymers801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2052
Polymers22,1251
Non-polymers801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.960, 36.078, 82.163
Angle α, β, γ (deg.)90.000, 100.000, 90.000
Int Tables number4
Space group name H-MP1211
Detailsmonomer,23.81 kD,92.1%

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Components

#1: Protein uncharacterized protein


Mass: 22125.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: CDC1873-00 / Gene: SP187300_1021 / Plasmid: pET15_NESG, SpR36-14.2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: B1RZQ2
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.08 Å3/Da / Density % sol: 40.77 %
Crystal growTemperature: 291 K / Method: microbatch crystallization under oil / pH: 10
Details: 40% PEG 8000, 0.1 M sodium bromide, 0.1 M CAPS, pH 10.0, Microbatch crystallization under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97907 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 3, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.548→50 Å / Num. all: 103638 / Num. obs: 100218 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 19.13 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 24.4
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 2.1 / Num. unique all: 10387 / % possible all: 94.2

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.548→36.946 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.13 / Phase error: 21.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.219 5063 5.06 %RANDOM
Rwork0.201 ---
obs0.201 100121 96.47 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.748 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso max: 75.7 Å2 / Biso mean: 26.629 Å2 / Biso min: 7.52 Å2
Baniso -1Baniso -2Baniso -3
1--3.104 Å2-0 Å20.414 Å2
2--8.014 Å2-0 Å2
3----4.91 Å2
Refinement stepCycle: LAST / Resolution: 1.548→36.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3075 0 2 295 3372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093198
X-RAY DIFFRACTIONf_angle_d1.4284328
X-RAY DIFFRACTIONf_chiral_restr0.127454
X-RAY DIFFRACTIONf_plane_restr0.006548
X-RAY DIFFRACTIONf_dihedral_angle_d15.8951196
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.548-1.5650.3821390.3293005314490
1.565-1.5840.321760.3013044322094
1.584-1.6030.2621800.2963097327795
1.603-1.6230.3411990.2773038323794
1.623-1.6450.2991450.2593148329394
1.645-1.6670.2871770.2563011318895
1.667-1.6910.2751580.2593202336095
1.691-1.7160.2851650.2433134329994
1.716-1.7430.2641490.2333075322495
1.743-1.7720.2821860.2353171335796
1.772-1.8020.2631760.2263103327995
1.802-1.8350.2251590.223079323896
1.835-1.870.2711640.2133209337396
1.87-1.9090.2391340.2093226336096
1.909-1.950.1721550.1913133328897
1.95-1.9950.2291750.2023243341897
1.995-2.0450.221440.2073139328397
2.045-2.1010.2231740.1953206338097
2.101-2.1620.2381650.1923216338198
2.162-2.2320.212020.193186338898
2.232-2.3120.2062210.1883113333498
2.312-2.4050.181590.1913308346798
2.405-2.5140.2011680.1873203337198
2.514-2.6470.211700.1953237340799
2.647-2.8120.2251750.23269344499
2.812-3.0290.2131850.1943200338599
3.029-3.3340.2041860.1953232341899
3.334-3.8160.2061580.183265342399
3.816-4.8060.1641400.1643307344799
4.806-36.9570.2261790.2223259343899
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)
11.83530.03030.13391.08060.19671.20780.06560.24330.0405-0.053-0.0151-0.07480.02430.0049-0.03440.10970.01670.00620.06310.01390.106721.490519.451263.3733
23.4356-0.0216-0.70631.364-0.33971.60480.20750.01560.0013-0.0337-0.06820.0470.0053-0.0113-0.11490.1156-0.01920.02110.146-0.02520.132550.622719.120958.5773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA-9 - 172
2X-RAY DIFFRACTION2chain BB-8 - 172

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