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- PDB-2p10: CRYSTAL STRUCTURE OF A PUTATIVE PHOSPHONOPYRUVATE HYDROLASE (MLL9... -

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Basic information

Entry
Database: PDB / ID: 2p10
TitleCRYSTAL STRUCTURE OF A PUTATIVE PHOSPHONOPYRUVATE HYDROLASE (MLL9387) FROM MESORHIZOBIUM LOTI MAFF303099 AT 2.15 A RESOLUTION
ComponentsMll9387 protein
KeywordsHYDROLASE / PUTATIVE PHOSPHONOPYRUVATE HYDROLASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


TIM-barrel domain, IGPS-like / Phosphoenolpyruvate hydrolase-like / Single helix bin / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle ...TIM-barrel domain, IGPS-like / Phosphoenolpyruvate hydrolase-like / Single helix bin / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Mll9387 protein
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_085906.1) from Mesorhizobium loti at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE, FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mll9387 protein
B: Mll9387 protein
C: Mll9387 protein
D: Mll9387 protein
E: Mll9387 protein
F: Mll9387 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,21229
Polymers186,8636
Non-polymers1,34923
Water12,827712
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29970 Å2
ΔGint-256 kcal/mol
Surface area53030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.269, 180.269, 185.514
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ARG / End label comp-ID: GLN / Refine code: 5 / Auth seq-ID: 9 - 283 / Label seq-ID: 10 - 284

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

#1: Protein
Mll9387 protein


Mass: 31143.910 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: NP_085906.1, mll9387 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q981G2
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 712 / 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: 3.1 Å3/Da / Density % sol: 60.36 %
Crystal growTemperature: 277 K / pH: 4
Details: NANODROP, 3.0% PEG 4000, 23.3% Glycerol, 0.1M Sodium acetate pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 4.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.918381, 0.979354
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 29, 2007
Details: 1M LONG RH COATED BENT CYLINDRICAL MIRROR FOR HORIZONTAL AND VERTICAL FOCUSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9183811
20.9793541
ReflectionResolution: 2.15→45.083 Å / Num. obs: 121425 / % possible obs: 99.3 % / Redundancy: 3.31 % / Biso Wilson estimate: 37.31 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.34
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
2.15-2.233.280.7641.641411199.6
2.23-2.320.618240111199.6
2.32-2.420.4852.538189199.7
2.42-2.550.3743.240952199.6
2.55-2.710.2884.240354199.6
2.71-2.920.196640561199.5
2.92-3.210.1248.940003199.6
3.21-3.670.06913.840334199.4
3.67-4.610.04419.440328199.2
4.61-45.10.0421.939992197.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.15→45.08 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.953 / SU B: 9.716 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.15
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. 4. ACETATE, GLYCEROL AND CHLORIDE ATOMS, PRESENT IN THE CRYSTALLIZATION SOLUTION, ARE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 6092 5 %RANDOM
Rwork0.162 ---
obs0.165 121409 99.3 %-
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: 43.89 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.07 Å20 Å2
2--0.13 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.15→45.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12016 0 82 712 12810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02212412
X-RAY DIFFRACTIONr_bond_other_d0.0010.028478
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.97816760
X-RAY DIFFRACTIONr_angle_other_deg0.888320648
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55651639
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70823.448522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.134152121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.37615108
X-RAY DIFFRACTIONr_chiral_restr0.0670.21901
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214022
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022482
X-RAY DIFFRACTIONr_nbd_refined0.2050.22787
X-RAY DIFFRACTIONr_nbd_other0.1890.29308
X-RAY DIFFRACTIONr_nbtor_refined0.1720.26218
X-RAY DIFFRACTIONr_nbtor_other0.0860.26601
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2624
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1180.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2740.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.40438290
X-RAY DIFFRACTIONr_mcbond_other0.46833325
X-RAY DIFFRACTIONr_mcangle_it2.283512819
X-RAY DIFFRACTIONr_scbond_it4.78984573
X-RAY DIFFRACTIONr_scangle_it6.594113920
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1533medium positional0.190.5
2B1533medium positional0.180.5
3C1533medium positional0.210.5
4D1533medium positional0.180.5
5E1533medium positional0.20.5
6F1533medium positional0.30.5
1A1618loose positional0.435
2B1618loose positional0.465
3C1618loose positional0.585
4D1618loose positional0.455
5E1618loose positional0.55
6F1618loose positional0.565
1A1533medium thermal0.962
2B1533medium thermal0.772
3C1533medium thermal0.882
4D1533medium thermal0.732
5E1533medium thermal0.722
6F1533medium thermal0.632
1A1618loose thermal2.7310
2B1618loose thermal2.310
3C1618loose thermal2.4910
4D1618loose thermal2.2310
5E1618loose thermal2.510
6F1618loose thermal2.4310
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 433 -
Rwork0.283 8561 -
obs--99.38 %
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)
10.31240.2759-0.14920.7175-0.54220.80570.05480.0780.0571-0.0173-0.0636-0.0869-0.09440.14290.0088-0.05170.01590.0419-0.06170.0411-0.098817.22339.3448.379
20.5818-0.446-0.12971.0584-0.04230.3261-0.0937-0.022-0.18180.00240.05160.16370.1167-0.0260.0421-0.0939-0.02450.0203-0.10330.0316-0.06660.59962.585-19.634
30.7805-0.09190.47291.6135-0.77841.58720.0731-0.09730.12890.41610.17120.6441-0.1428-0.291-0.24440.08520.02940.269-0.06160.10260.2871-16.29659.53916.409
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 2849 - 285
2X-RAY DIFFRACTION1BB9 - 28510 - 286
3X-RAY DIFFRACTION2CC9 - 28410 - 285
4X-RAY DIFFRACTION2DD9 - 28410 - 285
5X-RAY DIFFRACTION3EE9 - 28310 - 284
6X-RAY DIFFRACTION3FF9 - 28310 - 284

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