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- PDB-3g16: Crystal structure of protein of unknown function with cystatin-li... -

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Basic information

Entry
Database: PDB / ID: 3g16
TitleCrystal structure of protein of unknown function with cystatin-like fold (YP_001022489.1) from METHYLOBIUM PETROLEOPHILUM PM1 at 1.45 A resolution
Componentsuncharacterized protein with cystatin-like fold
Keywordsstructural genomics / unknown function / YP_001022489.1 / protein of unknown function with cystatin-like fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / Unknown ligand / SnoaL-like domain-containing protein
Function and homology information
Biological speciesMethylibium petroleiphilum PM1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of protein of unknown function with cystatin-like fold (YP_001022489.1) from METHYLOBIUM PETROLEOPHILUM PM1 at 1.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein with cystatin-like fold
B: uncharacterized protein with cystatin-like fold
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,27010
Polymers34,9442
Non-polymers3268
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-61 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.560, 68.450, 107.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsCRYSTAL PACKING ANALYSIS AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUGGEST THAT A DIMER IS THE STABLE OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein uncharacterized protein with cystatin-like fold


Mass: 17472.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylibium petroleiphilum PM1 (bacteria)
Gene: Mpe_A3301, YP_001022489.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A2SL15
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.56 Å3/Da / Density % sol: 51.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.0000M LiCl, 20.0000% PEG-6000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97864,0.97817
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 12, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978641
30.978171
ReflectionResolution: 1.45→27.973 Å / Num. obs: 63677 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.269 Å2 / Rmerge(I) obs: 0.025 / Net I/σ(I): 16.47
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.45-1.50.37421983410613188.8
1.5-1.560.2712.82299812218198.9
1.56-1.630.1923.92274012059198.9
1.63-1.720.1365.42428412812199.2
1.72-1.830.0918.22353812401199.2
1.83-1.970.05612.72290912037198.9
1.97-2.170.03520.12343912257198.9
2.17-2.480.02626.72300611971198.6
2.48-3.120.01935.12343612103198.5
3.12-27.9730.01447.22355012025197.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.45→27.973 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.695 / SU ML: 0.033 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.054
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.CHLORIDE (CL) FROM THE CRYSTALLIZATION AND GLYCEROL (GOL) FROM THE CRYOPROTECTION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5.AN UNIDENTIFIED LIGAND (UNL) HAS BEEN MODELED IN THE PUTATIVE ACTIVE SITE IN BOTH PROTEIN MOLECULES. IT IS POSSIBLE THAT THIS UNL IS ACTUALLY A PARTIALLY OCCUPIED MES MOLECULE FROM THE CRYSTALLIZATION BUFFER. THIS INFERENCE IS BASED ON THE LOWER B-FACTOR OF ATOM O7 OF UNL-1 WHICH SUGGESTS THAT THIS MAY BE A HEAVIER ATOM (LIKE SULFUR). 6.RESIDUES 45-48 IN CHAIN B HAVE POOR ELECTRON DENSITY AND AND HAVE BEEN MODELED BASED ON THE CORRESPONDING REGION OF CHAIN A.
RfactorNum. reflection% reflectionSelection details
Rfree0.167 3217 5.1 %RANDOM
Rwork0.148 ---
obs0.149 63622 99.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 68.37 Å2 / Biso mean: 20.701 Å2 / Biso min: 9.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2---0.46 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.45→27.973 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 34 372 2806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222564
X-RAY DIFFRACTIONr_bond_other_d0.0020.021803
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.9413485
X-RAY DIFFRACTIONr_angle_other_deg0.92634321
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5355332
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.42921.68125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.32715412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9771531
X-RAY DIFFRACTIONr_chiral_restr0.0960.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022937
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02608
X-RAY DIFFRACTIONr_nbd_refined0.2260.2454
X-RAY DIFFRACTIONr_nbd_other0.2140.21950
X-RAY DIFFRACTIONr_nbtor_refined0.1880.21242
X-RAY DIFFRACTIONr_nbtor_other0.0860.21433
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.226
X-RAY DIFFRACTIONr_mcbond_it1.42121666
X-RAY DIFFRACTIONr_mcbond_other0.3442643
X-RAY DIFFRACTIONr_mcangle_it1.91132504
X-RAY DIFFRACTIONr_scbond_it1.721119
X-RAY DIFFRACTIONr_scangle_it2.6313968
LS refinement shellResolution: 1.452→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 234 -
Rwork0.23 4345 -
all-4579 -
obs--98.16 %
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)
10.3110.05990.05270.58520.1840.45790.01810.0017-0.0062-0.0049-0.0119-0.0280.0436-0.0194-0.0062-0.02250.0026-0.0008-0.02740.0054-0.030820.819653.437512.7363
20.42390.28760.20031.19880.47240.66450.0021-0.01930.1263-0.0333-0.09620.1821-0.0764-0.13450.0941-0.03460.021-0.0127-0.0124-0.0113-0.006410.512667.600218.5767
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 155
2X-RAY DIFFRACTION2B4 - 155

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