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- PDB-3d4r: CRYSTAL STRUCTURE OF a DUF2118 family protein (MMP0046) FROM METH... -

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Basic information

Entry
Database: PDB / ID: 3d4r
TitleCRYSTAL STRUCTURE OF a DUF2118 family protein (MMP0046) FROM METHANOCOCCUS MARIPALUDIS AT 2.20 A RESOLUTION
ComponentsDomain of Unknown Function from the Pfam-B_34464 Family
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


Lipocalin - #400 / Protein of unknown function DUF2118 / Uncharacterized protein conserved in archaea (DUF2118) / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Lipocalin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Similarity search - Component
Biological speciesMethanococcus maripaludis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Domain of Unknown Function from the Pfam-B_34464 Family (NP_987166.1) from Methanococcus maripaludis JJ (DSM 2067) at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2008Provider: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Domain of Unknown Function from the Pfam-B_34464 Family
B: Domain of Unknown Function from the Pfam-B_34464 Family
C: Domain of Unknown Function from the Pfam-B_34464 Family
D: Domain of Unknown Function from the Pfam-B_34464 Family
E: Domain of Unknown Function from the Pfam-B_34464 Family
F: Domain of Unknown Function from the Pfam-B_34464 Family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,60917
Polymers118,8826
Non-polymers72711
Water9,584532
1
E: Domain of Unknown Function from the Pfam-B_34464 Family
F: Domain of Unknown Function from the Pfam-B_34464 Family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9387
Polymers39,6272
Non-polymers3105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint7 kcal/mol
Surface area15300 Å2
MethodPISA
2
C: Domain of Unknown Function from the Pfam-B_34464 Family
D: Domain of Unknown Function from the Pfam-B_34464 Family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9206
Polymers39,6272
Non-polymers2924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint7 kcal/mol
Surface area15300 Å2
MethodPISA
3
A: Domain of Unknown Function from the Pfam-B_34464 Family
B: Domain of Unknown Function from the Pfam-B_34464 Family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7524
Polymers39,6272
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-1 kcal/mol
Surface area15980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.877, 109.858, 135.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
12B
22D
32F

NCS domain segments:

Component-ID: 1 / Beg label comp-ID: GLY / End label comp-ID: GLU / Refine code: 6 / Auth seq-ID: 10 - 150 / Label seq-ID: 29 - 169

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21CC
31EE
12BB
22DD
32FF

NCS ensembles :
ID
1
2
DetailsAUTHORS STATE THAT THE PROTOMER MAY FORM A DIMER BASED ON CRYSTAL PACKING ANALYSIS. ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIC STATE.

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Components

#1: Protein
Domain of Unknown Function from the Pfam-B_34464 Family


Mass: 19813.730 Da / Num. of mol.: 6 / Mutation: F74L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanococcus maripaludis (archaea) / Strain: JJ [DSM 2067] / Gene: NP_987166.1, MMP0046 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q6M171
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE STRAIN CLONED, ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE STRAIN CLONED, METHANOCOCCUS MARIPALUDIS JJ, DIFFERS FROM THE DATABASE SEQUENCE STRAIN, METHANOCOCCUS MARIPALUDIS S2. SEQUENCING OF THE CLONED CONSTRUCT SHOWS A LEUCINE AT POSITION 74 INSTEAD OF A PHENYLALANINE. THE LEUCINE AT POSITION 74 IS SUPPORTED BY THE ELECTRON DENSITY.

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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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 277 K
Details: 21.5% polyethylene glycol 3350, 0.214M ammonium citrate, 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: 0.91837,0.97929,0.97913
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 17, 2008 / 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
10.918371
20.979291
30.979131
ReflectionResolution: 2.2→28.94 Å / Num. obs: 68137 / % possible obs: 100 %
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 1.1 / % possible all: 100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3.004data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→28.94 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.816 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. EDO WAS MODELED BASED ON CRYO CONDITIONS. 4. RAMACHANDRAN OUTLIERS A50 AND C50 ARE IN GOOD DENSITY.
RfactorNum. reflection% reflection
Rfree0.236 3446 5.1 %
Rwork0.193 --
obs0.195 68065 100 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 30.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7362 0 47 532 7941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227716
X-RAY DIFFRACTIONr_bond_other_d0.0010.025188
X-RAY DIFFRACTIONr_angle_refined_deg1.7811.99210464
X-RAY DIFFRACTIONr_angle_other_deg0.951312722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8985983
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.23124.369325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17151329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7631529
X-RAY DIFFRACTIONr_chiral_restr0.1020.21168
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028575
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021562
X-RAY DIFFRACTIONr_nbd_refined0.2010.21175
X-RAY DIFFRACTIONr_nbd_other0.1930.25166
X-RAY DIFFRACTIONr_nbtor_refined0.1850.23609
X-RAY DIFFRACTIONr_nbtor_other0.0870.24116
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2428
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1970.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8411.54896
X-RAY DIFFRACTIONr_mcbond_other0.1621.51942
X-RAY DIFFRACTIONr_mcangle_it1.31527657
X-RAY DIFFRACTIONr_scbond_it1.96133266
X-RAY DIFFRACTIONr_scangle_it2.7874.52786
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1699loose positional0.665
12C1699loose positional0.675
13E1699loose positional1.165
21B1671loose positional0.885
22D1671loose positional0.885
23F1671loose positional1.595
11A1699loose thermal4.6810
12C1699loose thermal2.6210
13E1699loose thermal3.1910
21B1671loose thermal5.2910
22D1671loose thermal3.3110
23F1671loose thermal3.7410
LS refinement shellResolution: 2.2→2.26 Å
RfactorNum. reflection% reflection
Rfree0.352 224 -
Rwork0.279 4685 -
obs--99.86 %
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)
12.28570.7602-0.41411.3477-0.43381.42650.0401-0.2775-0.0737-0.0093-0.0328-0.04350.00020.2007-0.0074-0.16810.02640.0131-0.1322-0.0003-0.090435.76232.60758.1
21.79760.7933-1.04211.6108-1.20292.9603-0.07720.12380.0367-0.20950.0910.1876-0.0124-0.3026-0.0138-0.14590.0176-0.0342-0.1628-0.0332-0.075413.37134.06551.256
31.78790.34530.69972.16351.07591.9742-0.1058-0.34240.11210.25060.025-0.0175-0.164-0.31650.0807-0.01120.161-0.0006-0.1106-0.0235-0.106445.0698.97929.495
42.1851-0.23390.02471.5388-0.37014.22620.09550.00550.33550.1176-0.1552-0.2685-0.79580.21220.05970.12120.0075-0.0279-0.26670.0238-0.020862.97419.70518.899
52.61162.56972.38445.18892.66674.24880.2551-0.0813-0.25630.37920.0932-0.05740.83040.0582-0.34830.087-0.015-0.0432-0.15180.0133-0.117515.43112.00324.284
60.56270.4766-0.11445.5166-0.91471.4646-0.0640.04910-0.37160.10010.43630.1747-0.1512-0.03610.0389-0.1494-0.0818-0.16470.0232-0.12581.82119.775.419
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-7 - 15012 - 169
2X-RAY DIFFRACTION2BB-6 - 15013 - 169
3X-RAY DIFFRACTION3CC-7 - 15012 - 169
4X-RAY DIFFRACTION4DD-7 - 15012 - 169
5X-RAY DIFFRACTION5EE-2 - 15017 - 169
6X-RAY DIFFRACTION6FF-7 - 15012 - 169

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