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- PDB-2qiw: Crystal structure of a putative phosphoenolpyruvate phosphonomuta... -

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Basic information

Entry
Database: PDB / ID: 2qiw
TitleCrystal structure of a putative phosphoenolpyruvate phosphonomutase (ncgl1015, cgl1060) from corynebacterium glutamicum atcc 13032 at 1.80 A resolution
ComponentsPEP phosphonomutase
KeywordsTRANSFERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


carboxyvinyl-carboxyphosphonate phosphorylmutase / carboxyvinyl-carboxyphosphonate phosphorylmutase activity
Similarity search - Function
Phosphoenolpyruvate phosphomutase / ICL/PEPM domain / Single helix bin / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle ...Phosphoenolpyruvate phosphomutase / ICL/PEPM domain / Single helix bin / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / TIM Barrel / Alpha-Beta Barrel / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / PEP phosphonomutase and related enzymes
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative PEP phosphonomutase (NP_600288.1) from Corynebacterium glutamicum ATCC 13032 Kitasato at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: 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 1.4Jul 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 1.5Jan 25, 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
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 (0) 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: PEP phosphonomutase
B: PEP phosphonomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,33018
Polymers53,8072
Non-polymers1,52316
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-83 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.520, 94.560, 107.970
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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLY / End label comp-ID: ALA / Refine code: 6 / Auth seq-ID: 0 - 254 / Label seq-ID: 1 - 255

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PEP phosphonomutase


Mass: 26903.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Species: Corynebacterium glutamicum / Strain: DSM 20300, JCM 1318, LMG 3730, NCIMB 10025 / Gene: NP_600288.1, Cgl1060 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: Q8NRI8, carboxyvinyl-carboxyphosphonate phosphorylmutase

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Non-polymers , 6 types, 538 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


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


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 3.91 Å3/Da / Density % sol: 68.57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: NANODROP, 2.0M (NH4)2SO4, 2.0% PEG 400, 0.1M HEPES pH 7.5, 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, 0.97901, 0.97935
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 21, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979011
30.979351
ReflectionResolution: 1.8→29.45 Å / Num. obs: 78759 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.945 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 10.6
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.860.41122299314091199.4
1.86-1.940.3182.62641316214199.7
1.94-2.030.2293.52517715344199.9
2.03-2.130.1684.92321014131199.7
2.13-2.270.1276.22619815841199.7
2.27-2.440.0938.42433914662199.8
2.44-2.690.07410.22567015366199.7
2.69-3.070.04714.82489314820199.8
3.07-3.870.02922.82580815221199.7
3.87-29.450.02130.52598515029198.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.45 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / SU B: 3.233 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.075
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. PEG 400 (PG4), HEPES (EPE), SULFATE (SO4), AND GLYCEROL (GOL) ARE PRESENT IN THE CRYSTALLIZATION CRYO BUFFER, AND HAVE BEEN MODELED INTO THE STRUCTURE. 5. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED INTO THE PUTATIVE ACTIVE SITE ON SUBUNIT A. 6). UNEXPLAINED ELECTRON DENSITIES NEAR HIS 211 IN THE A SUBUNIT, ARG 136 IN THE A SUBUNIT, AND HIS 211 IN THE B SUBUNIT WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.168 3957 5 %RANDOM
Rwork0.144 ---
obs0.145 78697 99.81 %-
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: 25.066 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2---0.48 Å20 Å2
3---1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3736 0 97 522 4355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223979
X-RAY DIFFRACTIONr_bond_other_d0.0020.022571
X-RAY DIFFRACTIONr_angle_refined_deg1.571.9665424
X-RAY DIFFRACTIONr_angle_other_deg1.00536328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3745542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.25425.064156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.22415612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2971518
X-RAY DIFFRACTIONr_chiral_restr0.0950.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024495
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02739
X-RAY DIFFRACTIONr_nbd_refined0.220.2835
X-RAY DIFFRACTIONr_nbd_other0.2020.22823
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21979
X-RAY DIFFRACTIONr_nbtor_other0.0880.21910
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2407
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2960.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.221
X-RAY DIFFRACTIONr_mcbond_it2.00832749
X-RAY DIFFRACTIONr_mcbond_other0.5631067
X-RAY DIFFRACTIONr_mcangle_it2.51154122
X-RAY DIFFRACTIONr_scbond_it4.75981535
X-RAY DIFFRACTIONr_scangle_it6.768111285
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 3015 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.435
LOOSE THERMAL1.7510
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 290 -
Rwork0.206 5447 -
obs-5737 99.67 %
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)
10.5856-0.443-0.23251.20340.2630.5337-0.0461-0.0374-0.08740.06510.01110.09530.0795-0.01460.035-0.1508-0.00360.003-0.1634-0.0014-0.1764-9.2331.373-30.091
20.9487-0.0947-0.53010.8113-0.00950.8231-0.00770.03320.00840.01750.00570.1151-0.0158-0.09720.002-0.15890.0146-0.0094-0.1470.0015-0.1842-27.99461.102-15.501
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 2541 - 255
2X-RAY DIFFRACTION2BB0 - 2541 - 255

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