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- PDB-2ifx: Crystal structure of a putative 4-methylmuconolactone methylisome... -

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Basic information

Entry
Database: PDB / ID: 2ifx
TitleCrystal structure of a putative 4-methylmuconolactone methylisomerase (YP_295714.1) from Ralstonia eutropha JMP134 at 2.00 A resolution
ComponentsHypothetical protein
KeywordsStructural Genomics/Unknown function / YP_295714.1 / hypothetical protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Joint Center for Structural Genomics / JCSG / Structural Genomics-Unknown function COMPLEX
Function / homology4-Methylmuconolactone methyl-isomerase / Methylmuconolactone methyl-isomerase / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / MmlI domain-containing protein
Function and homology information
Biological speciesCupriavidus necator (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (YP_295714.1) from Ralstonia Eutropha JMP134 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Hypothetical protein
B: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4925
Polymers26,2732
Non-polymers2203
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-29 kcal/mol
Surface area10210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.060, 46.060, 124.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEPROAA1 - 112 - 12
21MSEPROBB1 - 112 - 12
32SERGLNAA15 - 4716 - 48
42SERGLNBB15 - 4716 - 48
53HISASPAA60 - 8261 - 83
63HISASPBB60 - 8261 - 83
74PHEALAAA101 - 107102 - 108
84PHEALABB101 - 107102 - 108

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Components

#1: Protein Hypothetical protein


Mass: 13136.301 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cupriavidus necator (bacteria) / Gene: YP_295714.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q471R3
#2: Chemical ChemComp-CL / CHLORIDE ION


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


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


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.59 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6
Details: 0.2M Ca(OAc)2, 20.0% PEG-8000, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.94926, 0.97925, 0.97939
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 11, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochrometer / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.949261
20.979251
30.979391
ReflectionResolution: 2→25.743 Å / Num. obs: 17384 / % possible obs: 94.7 % / Biso Wilson estimate: 44.084 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 10.34
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2-2.070.3282.55095270280
2.07-2.150.2253.65934308991.5
2.15-2.250.1614.66610342394.8
2.25-2.370.1325.66466335495.9
2.37-2.520.0947.46764345797.1
2.52-2.710.0769.76446335598
2.71-2.990.05612.76739347598.4
2.99-3.420.04216.26603341598.9
3.420.04318.96560342598.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→25.743 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 7.935 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.137
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. RESIDUES 49-51, 109-113 IN CHAIN A, AND 49-59, 108-113 IN CHAIN B ARE DISORDERED AND NOT INCLUDED IN THE MODEL. 4. GLYCEROL MOLECULES FROM THE CRYO SOLUTION ARE MODELED. 5. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 6. THERE ARE SOME UNEXPLAINED DENSITY NEAR RESIDUES B15(SER) AND B39(TYR). 7. SIGNIFICANT NCS DEVIATION OCCURS IN THE RESIDUE RANGE 83-100.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 882 5.1 %RANDOM
Rwork0.171 ---
obs0.173 17337 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.388 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2→25.743 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1638 0 13 125 1776
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221737
X-RAY DIFFRACTIONr_bond_other_d0.0010.021233
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9482344
X-RAY DIFFRACTIONr_angle_other_deg0.86132961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3785207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.78821.78684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.17415287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9421516
X-RAY DIFFRACTIONr_chiral_restr0.0730.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02398
X-RAY DIFFRACTIONr_nbd_refined0.2090.2319
X-RAY DIFFRACTIONr_nbd_other0.1980.21260
X-RAY DIFFRACTIONr_nbtor_refined0.190.2809
X-RAY DIFFRACTIONr_nbtor_other0.0880.2890
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2118
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.211
X-RAY DIFFRACTIONr_mcbond_it2.03731252
X-RAY DIFFRACTIONr_mcbond_other0.4093411
X-RAY DIFFRACTIONr_mcangle_it2.59251635
X-RAY DIFFRACTIONr_scbond_it4.7298826
X-RAY DIFFRACTIONr_scangle_it6.07111705
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1000 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.615
LOOSE THERMAL1.7610
LS refinement shellResolution: 1.999→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 65 -
Rwork0.236 1156 -
obs-1221 97.76 %
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)
13.98220.3629-1.024.24990.29212.73950.1250.05640.4287-0.0188-0.15450.214-0.16160.0340.0295-0.1006-0.02370.0264-0.29920.0065-0.11689.2114.98767.344
22.44360.8345-1.17574.3942-0.24665.1645-0.0828-0.0246-0.052-0.274-0.03730.17090.2894-0.30190.1201-0.2208-0.03830.0199-0.278-0.0238-0.08220.05321.53575.451
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 481 - 49
21AA53 - 10854 - 109
32BB0 - 481 - 49
42BB60 - 10761 - 108

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