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- PDB-4mve: Crystal structure of Tcur_1030 protein from Thermomonospora curvata -

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Basic information

Entry
Database: PDB / ID: 4mve
TitleCrystal structure of Tcur_1030 protein from Thermomonospora curvata
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homologyGXWXG domain / Domain of unknown function DUF4334 / GXWXG domain / GXWXG protein / Domain of unknown function (DUF4334) / Lipocalin / Beta Barrel / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesThermomonospora curvata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.11 Å
AuthorsMichalska, K. / Li, H. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of Tcur_1030 protein from Thermomonospora curvata
Authors: Michalska, K. / Li, H. / Endres, M. / Joachimiak, A.
History
DepositionSep 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Source and taxonomy

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)34,8642
Polymers34,8642
Non-polymers00
Water1,74797
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)17,4321
Polymers17,4321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)17,4321
Polymers17,4321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.803, 66.803, 127.368
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-207-

HOH

DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Uncharacterized protein


Mass: 17431.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomonospora curvata (bacteria) / Strain: DSM 43183 / Gene: Tcur_1030 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli)
Strain (production host): BL21(DE3) Gold carrying modified pGro7 plasmid
References: UniProt: D1A7M7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES/NaOH, 20%(w/v) PEG 4000 10%(w/v) 2-propanol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 28, 2013 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 19671 / Num. obs: 19664 / % possible obs: 99.96 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 36.54 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 12.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.764 / Mean I/σ(I) obs: 2.13 / Num. unique all: 978 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXmodel building
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
Cootmodel building
BUSTER2.10.0refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.11→29.58 Å / Cor.coef. Fo:Fc: 0.9527 / Cor.coef. Fo:Fc free: 0.9424 / SU R Cruickshank DPI: 0.185 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 1004 5.13 %RANDOM
Rwork0.1756 ---
all0.1771 19579 --
obs0.1771 19579 99.97 %-
Displacement parametersBiso mean: 40.77 Å2
Baniso -1Baniso -2Baniso -3
1-1.401 Å20 Å20 Å2
2--1.401 Å20 Å2
3----2.8021 Å2
Refine analyzeLuzzati coordinate error obs: 0.257 Å
Refinement stepCycle: LAST / Resolution: 2.11→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2351 0 0 97 2448
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0122397HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.033234HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1128SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes59HARMONIC2
X-RAY DIFFRACTIONt_gen_planes356HARMONIC5
X-RAY DIFFRACTIONt_it2397HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.78
X-RAY DIFFRACTIONt_other_torsion2.84
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion296SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2741SEMIHARMONIC4
LS refinement shellResolution: 2.11→2.22 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2258 127 4.47 %
Rwork0.1929 2712 -
all0.1944 2839 -
obs-2839 99.97 %
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)
13.64310.23952.2142.7729-0.94664.2861-0.2332-0.46960.38360.3846-0.05910.0394-0.3553-0.47310.2924-0.01210.0091-0.099-0.1142-0.0638-0.0131-8.023821.176228.5686
2-0.1621-0.63072.34052.6782-1.520.0907-0.05820.0566-0.04650.1627-0.13420.1070.1110.03820.19230.053-0.0047-0.0384-0.06840.01740.0857-1.868510.113327.2875
32.3515-0.10370.57994.95070.97074.7357-0.16030.15640.05080.00550.1961-0.26480.20960.3637-0.0358-0.1236-0.0432-0.0123-0.01790.01340.01472.167411.938517.419
43.7698-0.36011.03141.9755-0.75013.2281-0.09870.13090.0829-0.0394-0.042-0.30310.07410.35450.1406-0.0547-0.0278-0.029-0.05340.0148-0.0347-2.533511.728413.499
52.4817-1.33622.0719-0.40751.91295.88-0.0154-0.06230.19330.1926-0.0915-0.21630.0292-0.06350.1068-0.0164-0.0221-0.0715-0.10760.0021-0.0057-7.092316.577922.4026
63.82770.2937-0.90274.84280.20673.04170.00720.43580.2621-0.5663-0.01720.4813-0.4477-0.21810.010.02490.038-0.1088-0.07930.0094-0.0604-27.661319.6178-6.4567
70.1625-0.18462.73624.4040.34040.14240.04350.4470.0432-0.5474-0.0063-0.12770.20860.0207-0.03710.0457-0.02250.0093-0.0107-0.0453-0.0783-22.6425.9493-6.8427
83.7171.46182.59633.9096-0.19720.92710.0094-0.1846-0.03630.16610.0890.15480.05260.0643-0.0984-0.0405-0.01290.0246-0.0535-0.0138-0.0308-25.18033.43416.2214
91.15771.7961.43822.95371.61461.2515-0.13490.0962-0.23830.09320.0623-0.09920.14890.02530.0726-0.0174-0.0240.0335-0.0059-0.03610.0582-21.5883-1.48542.2205
101.389-0.73491.29222.23980.16392.4811-0.03370.10150.0568-0.1481-0.02270.0831-0.04860.05070.0565-0.0162-0.0114-0.0053-0.0464-0.0063-0.0278-21.304613.33540.681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|40 }A1 - 40
2X-RAY DIFFRACTION2{ A|41 - A|54 }A41 - 54
3X-RAY DIFFRACTION3{ A|55 - A|69 }A55 - 69
4X-RAY DIFFRACTION4{ A|70 - A|114 }A70 - 114
5X-RAY DIFFRACTION5{ A|115 - A|148 }A115 - 148
6X-RAY DIFFRACTION6{ B|1 - B|36 }B1 - 36
7X-RAY DIFFRACTION7{ B|37 - B|60 }B37 - 60
8X-RAY DIFFRACTION8{ B|61 - B|72 }B61 - 72
9X-RAY DIFFRACTION9{ B|73 - B|97 }B73 - 97
10X-RAY DIFFRACTION10{ B|98 - B|148 }B98 - 148

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