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- PDB-5olw: 5-fluorotryptophan labeled beta-phosphoglucomutase in an open con... -

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Basic information

Entry
Database: PDB / ID: 5olw
Title5-fluorotryptophan labeled beta-phosphoglucomutase in an open conformation
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / phosphoryl transfer / NMR labeling / 19F-NMR
Function / homology
Function and homology information


beta-phosphoglucomutase / beta-phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Beta-phosphoglucomutase / Beta-phosphoglucomutase hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...Beta-phosphoglucomutase / Beta-phosphoglucomutase hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsBowler, M.W. / von Velsen, J.
CitationJournal: Chem Sci / Year: 2017
Title: Observing enzyme ternary transition state analogue complexes by19F NMR spectroscopy.
Authors: Ampaw, A. / Carroll, M. / von Velsen, J. / Bhattasali, D. / Cohen, A. / Bowler, M.W. / Jakeman, D.L.
History
DepositionJul 28, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_auth_seq_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.conn_type_id / _struct_conn.id / _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_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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-phosphoglucomutase
B: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4097
Polymers50,2092
Non-polymers2005
Water3,729207
1
A: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2655
Polymers25,1041
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1452
Polymers25,1041
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.005, 73.971, 120.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11B-468-

HOH

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Components

#1: Protein Beta-phosphoglucomutase / / Beta-PGM


Mass: 25104.459 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (strain IL1403) (lactic acid bacteria)
Strain: IL1403 / Gene: pgmB, LL0429, L0001 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71447, beta-phosphoglucomutase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.75 Å3/Da / Density % sol: 55.3 % / Description: large square plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M calcium chloride dihydrate, 20% w/v PEG 6000 and 0.1M Tris
PH range: 7-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 4, 2016 / Details: beryllium CRL
RadiationMonochromator: C110 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.28→60.22 Å / Num. obs: 25484 / % possible obs: 99.7 % / Observed criterion σ(F): 3 / Redundancy: 3.9 % / CC1/2: 0.99 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.069 / Net I/σ(I): 8.9
Reflection shellResolution: 2.28→2.35 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2323 / CC1/2: 0.915 / Rpim(I) all: 0.36 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2whe

2whe


Resolution: 2.28→19.865 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2617 1280 5.04 %
Rwork0.2042 --
obs0.207 25374 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.28→19.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3478 0 5 207 3690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113640
X-RAY DIFFRACTIONf_angle_d1.2874947
X-RAY DIFFRACTIONf_dihedral_angle_d15.2412205
X-RAY DIFFRACTIONf_chiral_restr0.067549
X-RAY DIFFRACTIONf_plane_restr0.008647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2801-2.37120.31131440.252621X-RAY DIFFRACTION100
2.3712-2.4790.3071420.23072648X-RAY DIFFRACTION100
2.479-2.60940.29021490.22712619X-RAY DIFFRACTION100
2.6094-2.77250.30131340.23342664X-RAY DIFFRACTION99
2.7725-2.98590.30051330.23332645X-RAY DIFFRACTION100
2.9859-3.28520.29341530.23492667X-RAY DIFFRACTION99
3.2852-3.75770.30851330.22592676X-RAY DIFFRACTION99
3.7577-4.72380.19821470.16432712X-RAY DIFFRACTION99
4.7238-19.86620.22071450.17022842X-RAY DIFFRACTION99
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)
16.0182-1.5918-2.09882.03521.32921.8914-0.1634-0.0763-0.3521-0.2661-0.0747-0.0320.20890.40240.1320.34520.05130.0530.34380.00850.239138.3738-27.5659-14.3801
23.29781.41811.5792.58381.19053.66190.08620.04660.8226-0.4219-0.36430.1136-0.2868-0.6750.22230.3196-0.00420.03620.3556-0.12260.258713.3718-24.8289-11.0319
32.35650.16561.44891.33630.04652.14860.1571-0.0532-0.35030.0408-0.0711-0.05990.7457-0.5821-0.0390.3722-0.086-0.01780.473-0.05940.275310.564-33.9213-12.6523
46.39214.46782.95853.51782.09052.8368-0.69370.5130.6789-0.7160.2390.6026-0.1050.09430.4260.4577-0.0277-0.01250.29790.00260.341113.5815-22.9283-20.275
53.4587-1.3729-0.45892.14020.26821.6615-0.03050.13840.5198-0.529-0.0493-0.2931-0.00090.14920.06930.2845-0.00190.05050.22510.01040.238937.4648-20.7035-16.6602
61.2943-0.3846-0.20781.4473-0.49981.37890.0070.1049-0.2212-0.1918-0.0362-0.15690.46640.24450.1120.44560.02490.06990.3474-0.03890.276439.3591-36.1267-15.6194
76.1509-4.4318-2.03055.67940.91953.6999-0.3079-0.30720.00810.1952-0.02380.04040.56010.61190.13530.40710.14350.040.5888-0.0140.290453.4448-37.0791-11.1753
83.06120.9873-0.71870.3297-0.55881.7915-0.1229-0.25720.069-0.2425-0.0112-0.00690.20560.2619-0.03610.28820.02430.07950.25890.02190.430838.16174.8198-11.4163
92.9236-0.2942-2.18310.39570.46871.77470.1342-0.68570.9542-0.1151-0.05420.114-0.96811.33560.00070.4745-0.28810.02270.71950.00910.5353.46712.682-8.3477
106.61234.7887-1.25124.251-0.75881.7019-0.6844-0.2984-0.5393-0.70450.2019-0.28240.50310.70950.30740.2537-0.01790.04810.4340.00580.491851.65341.4174-15.8105
112.6477-1.0685-0.00372.4329-0.29941.7191-0.05460.33790.1335-0.4252-0.0473-0.07080.0908-0.13150.17830.2697-0.07670.04990.2865-0.00820.381327.4227-0.6611-17.8493
121.4301-0.45580.18022.60290.27262.4780.04010.41740.5145-0.2256-0.0542-0.1919-0.392-0.0459-0.00110.3065-0.03630.02410.28560.13490.428222.254615.1502-17.5463
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 30 )
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 65 )
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 86 )
5X-RAY DIFFRACTION5chain 'A' and (resid 87 through 141 )
6X-RAY DIFFRACTION6chain 'A' and (resid 142 through 208 )
7X-RAY DIFFRACTION7chain 'A' and (resid 209 through 224 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 30 )
9X-RAY DIFFRACTION9chain 'B' and (resid 31 through 65 )
10X-RAY DIFFRACTION10chain 'B' and (resid 66 through 86 )
11X-RAY DIFFRACTION11chain 'B' and (resid 87 through 140 )
12X-RAY DIFFRACTION12chain 'B' and (resid 141 through 224 )

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