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- PDB-6eep: Crystal Structure of Ribose-5-phosphate Isomerase from Legionella... -

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Basic information

Entry
Database: PDB / ID: 6eep
TitleCrystal Structure of Ribose-5-phosphate Isomerase from Legionella pneumophila
ComponentsRibose-5-phosphate isomerase A
KeywordsISOMERASE / SSGCID / pentose phosphate pathway / ribose-5-phosphate / ribulose-5-phosphate / carbohydrate degradation / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


D-ribose metabolic process / ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch / cytosol
Similarity search - Function
Ribose-5-phosphate isomerase, type A, subgroup / Ribose 5-phosphate isomerase, type A / Ribose 5-phosphate isomerase A (phosphoriboisomerase A) / Rossmann fold - #1360 / ACT domain / NagB/RpiA transferase-like / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribose-5-phosphate isomerase A
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Ribose-5-phosphate Isomerase from Legionella pneumophila
Authors: Braverman, K.N. / Dranow, D.M. / Mayclin, S.J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionAug 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribose-5-phosphate isomerase A
B: Ribose-5-phosphate isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6904
Polymers46,6442
Non-polymers462
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-38 kcal/mol
Surface area16770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.630, 67.930, 74.000
Angle α, β, γ (deg.)90.000, 119.540, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-613-

HOH

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Components

#1: Protein Ribose-5-phosphate isomerase A / Phosphoriboisomerase A / PRI


Mass: 23321.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: rpiA, lpg0094 / Plasmid: LepnA.00944.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5ZZB7, ribose-5-phosphate isomerase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.38 Å3/Da / Density % sol: 48.23 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: LepnA.00944.a.B1.PS38423 at 22.85 mg/ml was mixed 1:1 with MCSG1(B8): 25.5% (w/v) PEG-4,000, 15% (v/v) Glycerol, 0.085 M Tris Base / Hydrochloric, 0.17 M Sodium Acetate, pH = 8.5. Tray: 300294b8. Puck: jve-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 28, 2018 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→32.19 Å / Num. obs: 37853 / % possible obs: 97.7 % / Redundancy: 4.117 % / Biso Wilson estimate: 33.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.067 / Χ2: 0.977 / Net I/σ(I): 13.97 / Num. measured all: 155837 / Scaling rejects: 30
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.85-1.94.2420.5482.5428200.8130.62697.3
1.9-1.954.2790.4143.3526750.8840.47397.4
1.95-2.014.2660.3234.3526360.9180.36997.9
2.01-2.074.2590.2395.7625710.9540.27397.9
2.07-2.144.2430.1986.8524720.970.22797.6
2.14-2.214.2250.1668.2524010.9760.1998.1
2.21-2.294.1840.1399.7323310.9810.15997.9
2.29-2.394.1760.11611.2122430.9880.13497.6
2.39-2.494.1460.10212.5721670.9910.11897.9
2.49-2.624.1020.08115.0820380.9930.09397.8
2.62-2.764.040.06517.3919680.9950.07598.3
2.76-2.933.9960.05620.1718430.9960.06597.8
2.93-3.133.9780.0522.8417570.9960.05897.8
3.13-3.383.9580.04425.8516040.9960.05197.2
3.38-3.73.9060.03928.4915030.9970.04597.3
3.7-4.143.9030.03629.8313550.9980.04198
4.14-4.783.8710.03431.0811860.9970.0496.9
4.78-5.853.880.03130.910250.9970.03698.7
5.85-8.273.8520.03230.758160.9970.03798.7
8.27-32.193.6470.03231.974420.9970.03795.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.14_3219)refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X84

4x84


Resolution: 1.85→32.19 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.01
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 2210 6.12 %random
Rwork0.1578 ---
obs0.1613 36108 93.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.24 Å2 / Biso mean: 30.0075 Å2 / Biso min: 11.15 Å2
Refinement stepCycle: final / Resolution: 1.85→32.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3219 0 2 431 3652
Biso mean--35.04 38.75 -
Num. residues----435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.89030.28681390.22591857199683
1.8903-1.93420.2911220.21851924204685
1.9342-1.98260.23081340.2012035216990
1.9826-2.03620.24881400.18442027216791
2.0362-2.09610.24961510.18222067221892
2.0961-2.16370.25931360.17112074221093
2.1637-2.2410.20521360.17632142227894
2.241-2.33070.23471180.16062141225994
2.3307-2.43680.2371500.17922126227695
2.4368-2.56520.24411470.17582164231196
2.5652-2.72590.2531550.16912160231596
2.7259-2.93620.21221280.17112200232897
2.9362-3.23140.22721410.16622209235097
3.2314-3.69840.18431400.14462230237097
3.6984-4.65740.1941400.12322219235998
4.6574-32.19530.17791330.13552323245699
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)
14.1874-0.5883-3.66466.68610.66363.23440.00110.1301-0.62180.1049-0.2388-0.02080.0566-0.03550.15690.186-0.0225-0.02080.1324-0.00040.184315.5246-7.325412.2857
25.1376-0.33993.9360.3655-0.00543.1710.3593-0.5783-0.85160.139-0.0589-0.0030.3301-0.183-0.25730.2917-0.00960.00160.18660.06930.261910.0306-14.736816.3365
32.5906-0.37930.84180.6814-0.0660.9889-0.2071-0.46170.3530.23880.0701-0.002-0.2155-0.02260.13240.21380.0007-0.00850.2256-0.0550.19094.34725.176623.7097
45.9224-1.679-2.87465.27761.28234.94980.0924-0.11360.6375-0.30390.0138-0.3752-0.7280.0669-0.12430.24730.0088-0.07110.1510.02630.24190.141211.409313.3467
52.4276-0.49720.59171.3416-0.22591.7121-0.1028-0.56820.3360.2119-0.0512-0.0127-0.2239-0.09340.15490.23770.011-0.01980.2696-0.07430.203-2.4545.895925.3831
63.87295.51750.63878.15480.94454.1230.6588-1.6555-0.34691.2347-0.6478-0.79480.10270.2376-0.00760.37280.0258-0.15910.5481-0.04730.326919.75461.602234.985
77.5726-0.7708-1.01817.5627-1.02116.81660.1304-0.2105-0.324-0.5176-0.12430.89570.2739-0.66470.06910.1512-0.0322-0.04390.26220.03480.3212-35.9548-1.5117-0.4299
87.8631-3.9943-0.63472.2661-0.30897.8367-0.11390.30950.49240.1381-0.04090.6451-0.7111-0.43570.10180.1770.0322-0.05390.2108-0.02180.3531-27.084211.8291.986
95.48740.36710.57225.7498-2.97175.8373-0.1140.12720.4558-0.2390.13780.3915-0.3436-0.4097-0.04260.18420.0304-0.01810.153-0.02410.1751-27.3977.5449-3.7025
108.7255-7.71056.56767.3263-6.1875.47330.22840.4197-0.0678-0.3122-0.217-0.0111-0.19230.6137-0.03020.2153-0.01070.02520.1551-0.0290.2092-18.09723.9768-4.5351
117.6971.14253.35961.5465-0.88232.9001-0.0945-0.17350.4678-0.04590.04890.36-0.30120.0448-0.01770.27610.0462-0.01780.1337-0.02930.3258-17.976414.34673.0929
125.92580.29420.29546.8726-1.85794.0208-0.0079-0.4445-0.12590.30510.05880.4546-0.0059-0.3402-0.03360.1425-0.01440.00460.1968-0.03880.1817-26.3885-2.074212.6811
133.8588-0.1811.11132.0658-0.82891.4567-0.0024-0.156-0.11210.06820.01730.23430.0872-0.2227-0.01330.1753-0.0190.03460.1756-0.02140.1361-23.0319-2.377111.5697
144.1963.9065-5.03373.615-4.66446.13070.1052-0.3436-0.6887-0.07930.0091-0.30050.29260.0167-0.0210.2573-0.0338-0.00750.21680.06320.2588-4.3442-12.577219.1841
151.51160.02760.13972.43380.36645.5769-0.09220.0304-0.4046-0.2979-0.2321-0.1970.79940.09640.31610.26480.04480.0570.1632-0.01810.2645-9.9163-11.83328.9166
163.5564-0.83650.61071.5303-0.72082.37440.0606-0.4181-0.04570.1615-0.07290.1120.0495-0.24110.01240.213-0.04190.02650.2237-0.0080.1636-16.7768-5.414319.5444
176.79872.79765.06098.53714.71475.03360.0554-0.6810.38440.1423-0.45211.01890.011-1.53020.39140.2087-0.0130.0150.4319-0.02840.3903-38.9611-1.05389.4031
185.21521.32892.43415.60191.00535.5445-0.1068-0.2656-0.1415-0.0040.1527-0.30120.09940.3146-0.0290.1490.03070.03080.25860.02230.152721.1184-4.482324.3166
196.9659-5.0591-3.73974.21024.39597.2107-0.0704-0.2672-0.11260.30330.0829-0.43570.3980.4343-0.02840.1733-0.0086-0.02840.26820.01590.227223.4216-5.686718.6395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 44 through 61 )B44 - 61
2X-RAY DIFFRACTION2chain 'B' and (resid 62 through 75 )B62 - 75
3X-RAY DIFFRACTION3chain 'B' and (resid 76 through 147 )B76 - 147
4X-RAY DIFFRACTION4chain 'B' and (resid 148 through 164 )B148 - 164
5X-RAY DIFFRACTION5chain 'B' and (resid 165 through 202 )B165 - 202
6X-RAY DIFFRACTION6chain 'B' and (resid 203 through 216 )B203 - 216
7X-RAY DIFFRACTION7chain 'A' and (resid -1 through 15 )A-1 - 15
8X-RAY DIFFRACTION8chain 'A' and (resid 16 through 27 )A16 - 27
9X-RAY DIFFRACTION9chain 'A' and (resid 28 through 49 )A28 - 49
10X-RAY DIFFRACTION10chain 'A' and (resid 50 through 61 )A50 - 61
11X-RAY DIFFRACTION11chain 'A' and (resid 62 through 75 )A62 - 75
12X-RAY DIFFRACTION12chain 'A' and (resid 76 through 97 )A76 - 97
13X-RAY DIFFRACTION13chain 'A' and (resid 98 through 134 )A98 - 134
14X-RAY DIFFRACTION14chain 'A' and (resid 135 through 148 )A135 - 148
15X-RAY DIFFRACTION15chain 'A' and (resid 149 through 164 )A149 - 164
16X-RAY DIFFRACTION16chain 'A' and (resid 165 through 202 )A165 - 202
17X-RAY DIFFRACTION17chain 'A' and (resid 203 through 216 )A203 - 216
18X-RAY DIFFRACTION18chain 'B' and (resid 0 through 27 )B0 - 27
19X-RAY DIFFRACTION19chain 'B' and (resid 28 through 43 )B28 - 43

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