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- PDB-2qzg: Crystal structure of unknown function protein MMP1188 -

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Basic information

Entry
Database: PDB / ID: 2qzg
TitleCrystal structure of unknown function protein MMP1188
ComponentsConserved uncharacterized archaeal protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Methanococcus maripaludis / unknown function protein / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyUncharacterised protein family UPF0147 / Uncharacterised protein family (UPF0147) / Ta0600-like / Ta0600-like superfamily / de novo design (two linked rop proteins) / Up-down Bundle / Mainly Alpha / UPF0147 protein MMP1188
Function and homology information
Biological speciesMethanococcus maripaludis S2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 Å
AuthorsChang, C. / Perez, V. / Volkart, L. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of MMP1188, unknown function protein.
Authors: Chang, C. / Volkart, L. / Freeman, L. / Joachimiak, A.
History
DepositionAug 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 20, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved uncharacterized archaeal protein
B: Conserved uncharacterized archaeal protein
C: Conserved uncharacterized archaeal protein
D: Conserved uncharacterized archaeal protein


Theoretical massNumber of molelcules
Total (without water)42,6344
Polymers42,6344
Non-polymers00
Water2,198122
1
A: Conserved uncharacterized archaeal protein
C: Conserved uncharacterized archaeal protein


Theoretical massNumber of molelcules
Total (without water)21,3172
Polymers21,3172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
MethodPISA
2
B: Conserved uncharacterized archaeal protein
D: Conserved uncharacterized archaeal protein


Theoretical massNumber of molelcules
Total (without water)21,3172
Polymers21,3172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.753, 83.617, 54.583
Angle α, β, γ (deg.)90.00, 111.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Conserved uncharacterized archaeal protein


Mass: 10658.489 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis S2 (archaea) / Species: Methanococcus maripaludis / Strain: S2, LL / Gene: MMP1188 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6LY05
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Na Acetate, 18% PEG 4000, pH 4.6, 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: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 23, 2007
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.09→50 Å / Num. all: 22725 / Num. obs: 22678 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Biso Wilson estimate: 36.66 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 57.35
Reflection shellResolution: 2.09→2.12 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 6.13 / Num. unique all: 555 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.09→29.2 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.019 / SU ML: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26176 1162 5.1 %RANDOM
Rwork0.2085 ---
all0.21125 21491 --
obs0.21125 21491 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.423 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å2-1.56 Å2
2---1.31 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.09→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2745 0 0 122 2867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222799
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9613806
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6285352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04526.241133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.62615514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1341516
X-RAY DIFFRACTIONr_chiral_restr0.0810.2458
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022081
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2060.21315
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21975
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.265
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9581.51844
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.26622901
X-RAY DIFFRACTIONr_scbond_it2.10731062
X-RAY DIFFRACTIONr_scangle_it3.4084.5905
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 68 -
Rwork0.223 1462 -
obs--92.95 %
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)
13.0824-0.2843.39492.94130.734612.45980.1578-0.5379-0.24880.41370.09760.41020.2805-0.6429-0.2554-0.1714-0.05280.0930.02390.044-0.173710.287139.06533.5767
23.919-2.76930.07875.1512-2.38243.5369-0.0143-0.38830.29170.2265-0.0009-0.4941-0.1235-0.05280.0151-0.1162-0.04430.0194-0.1123-0.0539-0.093719.070538.9293-0.293
34.1369-1.0673.33865.31660.990112.55920.09310.37540.2258-0.5116-0.23130.3542-1.22710.52020.13820.0090.03570.0438-0.24560.1189-0.021424.175350.0664-25.2923
44.8061-2.3902-2.17666.78382.89229.25770.31250.43370.0179-0.4078-0.48370.7867-0.222-0.35870.1712-0.13450.06980.0728-0.13680.0143-0.058720.645241.8764-21.7254
510.90833.46441.40617.14390.36312.89150.2927-0.798-0.61730.2167-0.13150.2507-0.07850.0882-0.1613-0.15650.0114-0.0826-0.19980.19360.005523.228415.53810.5294
66.8514-2.1853-3.35295.3722-0.75463.52810.28340.3286-0.6399-0.728-0.23160.50390.0091-0.1595-0.0518-0.0760.0403-0.1016-0.14890.0359-0.071821.236620.5656-7.2782
719.45816.54595.47765.96692.46114.69330.30021.5826-0.96070.25480.1654-0.24630.59190.4217-0.4656-0.03450.2563-0.02660.1289-0.1541-0.270940.126228.4357-25.6674
87.4296-1.11611.82022.4661-0.42274.74560.41530.1075-0.27780.5202-0.0766-0.28740.27790.3159-0.33870.00680.1083-0.0297-0.073-0.0209-0.213936.997331.2881-17.1849
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA9 - 4812 - 51
2X-RAY DIFFRACTION2AA49 - 9152 - 94
3X-RAY DIFFRACTION3BB9 - 4812 - 51
4X-RAY DIFFRACTION4BB49 - 9152 - 94
5X-RAY DIFFRACTION5CC9 - 4812 - 51
6X-RAY DIFFRACTION6CC49 - 9052 - 93
7X-RAY DIFFRACTION7DD9 - 4812 - 51
8X-RAY DIFFRACTION8DD49 - 9052 - 93

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