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- PDB-3lot: Crystal structure of PROTEIN OF UNKNOWN FUNCTION (NP_070038.1) fr... -

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Basic information

Entry
Database: PDB / ID: 3lot
TitleCrystal structure of PROTEIN OF UNKNOWN FUNCTION (NP_070038.1) from ARCHAEOGLOBUS FULGIDUS at 1.89 A resolution
Componentsuncharacterized protein
Keywordsstructure genomics / unknown function / PROTEIN OF UNKNOWN FUNCTION / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Prokaryotic protein of unknown function (DUF849)
Function / homology
Function and homology information


L-lysine catabolic process to acetate / transferase activity / metal ion binding
Similarity search - Function
3-keto-5-aminohexanoate cleavage enzyme / beta-keto acid cleavage enzyme / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Unknown ligand / Uncharacterized protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.89 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of PROTEIN OF UNKNOWN FUNCTION (NP_070038.1) from ARCHAEOGLOBUS FULGIDUS at 1.89 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 17, 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 1.5Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
C: uncharacterized protein
D: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,16317
Polymers142,8424
Non-polymers32113
Water26,3381462
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11430 Å2
ΔGint-202 kcal/mol
Surface area41090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.786, 103.079, 156.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A4 - 313
2116B4 - 313
3116C4 - 313
4116D4 - 313

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Components

#1: Protein
uncharacterized protein


Mass: 35710.473 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Gene: AF_1210 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: O29058
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 8 / Source method: obtained synthetically
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1462 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE 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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2000M ammonium acetate, 30.0000% polyethylene glycol 4000, 0.1M sodium citrate pH 5.6, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97936,0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 14, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979361
30.979221
ReflectionResolution: 1.89→48.97 Å / Num. obs: 98016 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.571 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 9.84
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.89-1.960.5522.2327689838197.9
1.96-2.040.4272.9349109847199.4
2.04-2.130.3343.7334909385199.5
2.13-2.240.2515350689594199.8
2.24-2.380.2125.9361119778199.8
2.38-2.560.1816.8357569660199.9
2.56-2.820.1349368529954199.8
2.82-3.230.08513.7368089947199.7
3.23-4.060.0521.6362149845199.1
4.06-48.970.0426.63701210168197.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.89→48.97 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 7.686 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.139
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS 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 RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.ACETATE ION FROM CRYSTALLIZATION AND ZN IONS FROM BACTERIAL NATURE PROCESSING ARE MODELED IN THE STRUCTURE, RESPECTIVELY. THE PRESENCE OF ZINC(ZN) AT THIS SITE IS SUPPORTED BY X-RAY FLUORESCENCE AND BINDING GEOMETRY. 5.UNKNOWN LIGANDS ARE MODELED NEAR THE METAL-BINDING SITE IN EACH SUBUNIT.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 4891 5 %RANDOM
Rwork0.156 ---
obs0.159 97971 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.83 Å2 / Biso mean: 16.386 Å2 / Biso min: 3.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2--1.34 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.89→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9690 0 39 1462 11191
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02210237
X-RAY DIFFRACTIONr_bond_other_d0.0010.027073
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.97713898
X-RAY DIFFRACTIONr_angle_other_deg0.945317305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38251312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33623.881438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.753151831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9671572
X-RAY DIFFRACTIONr_chiral_restr0.0930.21551
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111508
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022040
X-RAY DIFFRACTIONr_mcbond_it0.7581.56399
X-RAY DIFFRACTIONr_mcbond_other0.2371.52596
X-RAY DIFFRACTIONr_mcangle_it1.309210405
X-RAY DIFFRACTIONr_scbond_it2.40833838
X-RAY DIFFRACTIONr_scangle_it3.8824.53493
Refine LS restraints NCS

Ens-ID: 1 / Number: 3784 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.315
2BLOOSE POSITIONAL0.295
3CLOOSE POSITIONAL0.255
4DLOOSE POSITIONAL0.285
1ALOOSE THERMAL1.610
2BLOOSE THERMAL1.4310
3CLOOSE THERMAL1.3810
4DLOOSE THERMAL2.2910
LS refinement shellResolution: 1.89→1.939 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 367 -
Rwork0.257 6641 -
all-7008 -
obs--97.33 %
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)
10.66110.0075-0.10430.2824-0.01580.5024-0.0001-0.01040.04720.00860.00290.0254-0.0429-0.1157-0.00280.02430.01190.00430.02880.00010.0205-4.142257.145283.9114
20.59370.0725-0.01740.26620.00290.43140.01470.0177-0.02890.00280.0025-0.02180.0310.0483-0.01720.01740.0061-0.00170.0064-0.00290.003627.666739.3349123.3039
30.7882-0.03250.07290.2453-0.03460.46780.00660.0315-0.0175-0.01260.0017-0.02550.02290.0953-0.00830.01980.00490.00410.0202-0.00320.005929.857245.686680.7974
41.0947-0.03550.03630.23180.00890.3706-0.0184-0.0075-0.10910.0288-0.00530.05320.0166-0.06140.02380.0231-0.00830.00870.012-0.00590.0294-6.566929.4662116.3126
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 313
2X-RAY DIFFRACTION2B3 - 313
3X-RAY DIFFRACTION3C4 - 313
4X-RAY DIFFRACTION4D1 - 313

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