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- PDB-5br9: Crystal structure of an uncharacterized protein with similarity t... -

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Basic information

Entry
Database: PDB / ID: 5br9
TitleCrystal structure of an uncharacterized protein with similarity to peptidase YEAZ from Pseudomonas aeruginosa
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / SSGCID / Pseudomonas aeruginosa / Uncharacterized protein / peptidase YEAZ / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine modification / cytosol
Similarity search - Function
tRNA threonylcarbamoyl adenosine modification protein TsaB / Gcp-like domain / tRNA N6-adenosine threonylcarbamoyltransferase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
tRNA threonylcarbamoyladenosine biosynthesis protein TsaB
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of an uncharacterized protein with similarity to peptidase YEAZ from Pseudomonas aeruginosa
Authors: Abendroth, J. / Fairman, J.W. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMay 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation

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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
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)126,1745
Polymers126,1745
Non-polymers00
Water6,918384
1
A: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)50,4702
Polymers50,4702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-17 kcal/mol
Surface area18410 Å2
MethodPISA
2
B: Uncharacterized protein
C: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)50,4702
Polymers50,4702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-17 kcal/mol
Surface area17950 Å2
MethodPISA
3
E: Uncharacterized protein

E: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)50,4702
Polymers50,4702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area1400 Å2
ΔGint-17 kcal/mol
Surface area17300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.350, 201.940, 162.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Uncharacterized protein


Mass: 25234.791 Da / Num. of mol.: 5 / Fragment: PsaeA.17385.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: PA3685 / Plasmid: PsaeA.17385.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HXV5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.63 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: Microlytics MCSG1 A3: 10% PEG 8000, 200mM NaCl, 100mM Na2HPO4/ KH2PO4 pH 6.2; PsaeA.17385.a.B1.PS02242 at 20mg/ml; cryo: 20% EG in 2 steps; tray 260042a3, puck ges3-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 12, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 55527 / Num. obs: 55353 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 38 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.079 / Χ2: 0.978 / Net I/σ(I): 16.65 / Num. measured all: 277630
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.35-2.415.10.8320.5372.9820475404740450.6100
2.41-2.480.8870.4293.6720044396339600.47999.9
2.48-2.550.9260.3434.5519428385138480.38399.9
2.55-2.630.9350.3045.1718831372337160.3499.8
2.63-2.710.9580.2426.3818532366136560.2799.9
2.71-2.810.9680.2057.4317638349734890.22999.8
2.81-2.910.980.1629.517173340033950.1899.9
2.91-3.030.9870.12911.6116539326932670.14499.9
3.03-3.170.9920.114.5815846314531390.11299.8
3.17-3.320.9950.07718.4715152301130090.08699.9
3.32-3.50.9960.06521.6114560288728850.07299.9
3.5-3.720.9980.05425.913468269726900.0699.7
3.72-3.970.9980.04629.512756256225530.05199.6
3.97-4.290.9980.0433.2411788237923680.04499.5
4.29-4.70.9980.03636.6810941222422040.04199.1
4.7-5.250.9980.03636.479851200319980.0499.8
5.25-6.070.9980.03934.488679178217750.04499.6
6.07-7.430.9990.03237.367344151715130.03699.7
7.43-10.510.9990.02743.695666120011760.0398
10.510.9990.02642.9329197096670.02994.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameClassification
XDSdata reduction
XSCALEdata scaling
BALBESphasing
MOLREPphasing
PHASERphasing
PHENIXrefinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3r6m
Resolution: 2.35→48.222 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2057 2766 5 %Random selection
Rwork0.1609 52579 --
obs0.1632 55345 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.31 Å2 / Biso mean: 45.8076 Å2 / Biso min: 16.78 Å2
Refinement stepCycle: final / Resolution: 2.35→48.222 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7909 0 0 384 8293
Biso mean---42.35 -
Num. residues----1081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078255
X-RAY DIFFRACTIONf_angle_d1.0711310
X-RAY DIFFRACTIONf_chiral_restr0.0471285
X-RAY DIFFRACTIONf_plane_restr0.0061491
X-RAY DIFFRACTIONf_dihedral_angle_d14.8954902
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.39050.28691310.228826012732100
2.3905-2.4340.26641420.211626002742100
2.434-2.48080.25621450.183125852730100
2.4808-2.53150.23841210.184226402761100
2.5315-2.58650.22241250.185926342759100
2.5865-2.64670.2471390.176225862725100
2.6467-2.71280.25541400.182526032743100
2.7128-2.78620.2521460.195325862732100
2.7862-2.86820.26081460.194426282774100
2.8682-2.96070.23231350.195226102745100
2.9607-3.06650.2561370.18826082745100
3.0665-3.18930.2251530.181426282781100
3.1893-3.33440.21531480.170225992747100
3.3344-3.51010.25891050.170426902795100
3.5101-3.730.19741240.159426252749100
3.73-4.01780.18461560.140626332789100
4.0178-4.42190.16531310.121326442775100
4.4219-5.06120.14491580.12082639279799
5.0612-6.37430.18851440.148126822826100
6.3743-48.23240.17391400.15282758289898
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.21661.1946-2.35692.83940.89323.190.07980.16490.2154-0.21850.0993-0.1120.07530.1534-0.13210.27470.06230.04470.33370.01660.15272.48555.2713-19.5124
28.70651.27522.73912.4409-3.09576.4479-0.2218-1.0751-0.41411.07740.6248-0.3106-0.01820.196-0.37110.3060.035-0.00720.5136-0.02160.15739.126653.8147-15.6655
35.7703-1.97070.13349.5891-1.47241.6785-0.4688-0.2997-0.35750.64950.4883-0.78060.51580.37790.04240.34320.0970.04630.46230.01570.20743.835150.7499-9.7718
42.1521.2745-1.04490.8185-1.02772.4834-0.3029-0.1339-0.2528-0.00940.273-0.06060.43740.29330.0470.31270.08780.05210.30820.02110.2092-3.704848.221-19.6102
52.5019-1.1807-1.39421.41031.26461.8323-0.2126-0.1357-0.0897-0.02960.2282-0.07540.00180.2886-0.03640.1991-0.0142-0.02540.33360.02560.16528.008450.3829-33.4035
64.0109-1.6321-0.7133.71211.02112.91310.18160.2975-0.235-0.5551-0.14440.68120.0218-0.3198-0.00010.2983-0.0471-0.04180.32630.05790.14936.665247.8324-40.8527
71.9741-5.96030.45053.5039-0.35554.18750.24970.11021.5975-0.5172-0.4669-0.5057-0.2329-0.08180.02130.3519-0.07920.12290.4984-0.03490.250615.444151.9586-47.3283
82.2771-1.7705-1.13561.83660.29332.1215-0.0463-0.02440.1166-0.06390.1053-0.1734-0.11590.2546-0.06230.1701-0.05880.0010.2914-0.01580.17613.681249.5661-34.1874
92.72330.5810.58253.0432-0.37014.62130.16380.4383-0.38990.9783-0.00020.36790.6914-0.2543-0.1470.51550.0222-0.0080.4633-0.03480.2527-9.254247.726-29.2224
103.2903-0.4483-0.68023.05881.62956.8625-0.0480.249-0.30220.04030.1191-0.15240.3210.5441-0.03270.2835-0.0128-0.04570.3522-0.02330.219232.091332.0953-7.1822
111.72220.0490.6883.66291.86045.1949-0.00350.1634-0.06070.0546-0.05-0.25340.18920.4205-0.03680.18590.013-0.00510.29710.00660.189927.338831.3545-24.1288
122.1592.08160.96695.51860.69981.6515-0.07820.5589-0.0624-0.42960.1023-0.2223-0.26730.2922-0.01380.24620.0028-0.00050.4787-0.0090.210423.218431.463-33.4938
130.8230.35350.16464.54992.44686.7765-0.00280.032-0.06560.1493-0.1189-0.0303-0.024-0.04930.10490.15060.0130.00340.30920.0160.203426.237329.9143-23.3241
147.48532.53982.54056.22783.24569.05320.2801-0.67880.0257-0.0055-0.5330.5676-0.0051-0.3853-0.01840.2972-0.0884-0.01440.22230.04370.294916.470932.737813.4234
157.405-0.11912.54453.2851-0.87542.7678-0.3960.37420.0839-0.38010.10221.0399-0.75290.07020.30390.2735-0.0474-0.08010.22980.00850.48179.393135.926610.1372
163.86572.71562.9744.24634.00743.925-0.01690.2024-0.2186-0.7319-0.18890.9632-0.3739-0.74820.21380.4264-0.0759-0.14860.30080.04330.443912.919540.47034.2595
173.63630.9877-0.7433.5242-0.26651.4639-0.11540.2716-0.3512-0.3190.1020.07670.1424-0.07380.05660.2325-0.0715-0.03130.21520.01490.228320.693530.4755.9326
182.94172.36360.7893.61450.17830.52410.0115-0.1873-0.19960.24340.02470.22490.0661-0.0446-0.04240.22440.00170.04540.21210.02940.38289.455117.037714.0025
198.085-0.23924.24056.11493.29764.3574-0.1554-0.7654-0.50.49120.04530.47350.1553-0.4873-0.03790.238-0.06060.11930.27070.08730.53180.41759.687315.3264
203.29233.0770.20354.684-0.12780.2187-0.11780.0707-0.18170.15930.02910.2030.10180.01590.14880.2792-0.03750.02590.24510.00610.331412.146420.894413.2897
217.46333.33982.33524.066-1.85888.402-0.0675-0.0218-0.4395-0.34230.32750.20750.175-0.0818-0.15760.32720.03810.03750.15560.07030.4192-17.868935.3449-9.5888
222.42580.9099-2.6790.7424-1.10962.9054-0.42850.0718-0.0825-0.60310.15650.4408-0.140.636-0.17910.6322-0.03780.010.47950.03660.4623-21.178633.6225-18.2819
232.0902-0.6506-3.8395.80330.49289.05620.1120.5415-0.4563-0.3041-0.35140.8162-0.1002-0.9362-0.05760.32920.05-0.09440.28280.00580.495-22.094741.6061-16.1442
245.6107-1.63751.32076.5904-0.49683.74410.0586-0.1257-0.37710.0056-0.05420.07370.2546-0.00730.01520.33360.03390.11320.18570.07920.2559-12.637437.6773-7.8939
258.85211.4332-0.7833.5994-3.13493.88020.08230.8344-0.9187-0.54260.1278-0.25210.63140.7475-0.0720.45240.18690.05740.3722-0.01050.3371-6.464140.5657-13.7681
262.3896-1.69630.84858.8196-0.1941.5060.23720.0004-0.6657-0.4564-0.04410.08860.1654-0.0625-0.20970.27770.0275-0.04260.24960.03040.4397-10.066317.237-6.3193
271.4056-0.8670.32738.5463-0.48391.54310.2315-0.0187-0.5071-0.0567-0.048-0.0553-0.1174-0.0228-0.08760.28850.03940.02430.29120.080.3949-11.653624.9615-6.1713
283.45830.1708-1.05731.92051.45281.5495-0.03790.551-0.6520.1053-0.4727-0.55161.05811.19360.21840.20070.1823-0.00651.12370.36430.838440.1232-3.8876-14.4254
296.35060.61870.90584.05622.44016.85490.75990.0214-0.75350.575-0.78070.007-0.10581.41030.1280.71090.22090.10710.82550.17190.956336.2892-10.5333-13.8735
305.36360.74694.58127.5072-0.43234.73970.41020.7106-1.65390.13590.1010.03781.11031.1006-0.66950.55310.47830.03270.98880.36291.048942.7057-11.126-8.0134
315.1038-2.59131.89951.4271-0.95640.78880.0430.7717-0.4611-0.1559-0.3782-0.575-0.0741.20150.11240.3606-0.0209-0.00011.0180.24490.620538.90511.253-7.2212
325.05130.52381.67132.6923-0.62922.9715-0.07990.0394-0.6352-0.1426-0.2604-0.46490.1240.78460.18440.33320.03430.05360.33530.06990.384328.01712.0799-21.9494
337.04462.7339-3.00383.1136-2.05044.0622-0.340.4757-0.467-0.55610.0482-0.03580.10310.23050.24250.44260.00140.01130.2802-0.02220.335121.91337.5285-27.8553
344.91090.591.18152.5587-0.74484.6246-0.21140.3634-0.7677-0.48-0.0864-0.35240.11590.93360.30180.45320.03220.0830.4160.00630.460324.8981-1.4988-24.1921
352.6081.7953-0.24161.65090.35281.8320.2695-0.2753-0.5817-0.0538-0.9021-0.1404-0.82110.41410.3610.7914-0.164-0.19410.77610.30660.49133.892810.2531-10.7176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 20 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 34 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 50 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 51 through 86 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 87 through 131 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 132 through 148 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 149 through 159 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 160 through 200 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 201 through 216 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 86 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 87 through 131 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 132 through 160 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 161 through 216 )B0
14X-RAY DIFFRACTION14chain 'C' and (resid -1 through 12 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 13 through 34 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 35 through 50 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 51 through 86 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 87 through 148 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 149 through 172 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 173 through 216 )C0
21X-RAY DIFFRACTION21chain 'D' and (resid 1 through 20 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 21 through 38 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 39 through 50 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 51 through 68 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 69 through 86 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 87 through 172 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 173 through 214 )D0
28X-RAY DIFFRACTION28chain 'E' and (resid 1 through 20 )E0
29X-RAY DIFFRACTION29chain 'E' and (resid 21 through 35 )E0
30X-RAY DIFFRACTION30chain 'E' and (resid 36 through 50 )E0
31X-RAY DIFFRACTION31chain 'E' and (resid 51 through 86 )E0
32X-RAY DIFFRACTION32chain 'E' and (resid 87 through 131 )E0
33X-RAY DIFFRACTION33chain 'E' and (resid 132 through 160 )E0
34X-RAY DIFFRACTION34chain 'E' and (resid 161 through 200 )E0
35X-RAY DIFFRACTION35chain 'E' and (resid 201 through 216 )E0

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