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- PDB-6dur: Citrobacter freundii tyrosine phenol-lyase complexed with L-pheny... -

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Basic information

Entry
Database: PDB / ID: 6dur
TitleCitrobacter freundii tyrosine phenol-lyase complexed with L-phenylalanine
ComponentsTyrosine phenol-lyase
KeywordsLYASE / pyridoxal-5'-phosphate / aminotransferase fold
Function / homology
Function and homology information


tyrosine phenol-lyase / tyrosine phenol-lyase activity / tyrosine metabolic process
Similarity search - Function
Tyrosine phenol-lyase / Beta-eliminating lyase family / Tryptophanase, conserved site / Beta-eliminating lyases pyridoxal-phosphate attachment site. / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
: / Chem-P70 / Chem-P71 / TRIETHYLENE GLYCOL / Tyrosine phenol-lyase
Similarity search - Component
Biological speciesCitrobacter freundii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPhillips, R.S.
CitationJournal: Biochemistry / Year: 2018
Title: Crystal Structures of Wild-Type and F448A Mutant Citrobacter freundii Tyrosine Phenol-Lyase Complexed with a Substrate and Inhibitors: Implications for the Reaction Mechanism.
Authors: Phillips, R.S. / Craig, S.
History
DepositionJun 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _entity.formula_weight
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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.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.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 / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tyrosine phenol-lyase
B: Tyrosine phenol-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,0988
Polymers102,7552
Non-polymers1,3436
Water10,989610
1
A: Tyrosine phenol-lyase
B: Tyrosine phenol-lyase
hetero molecules

A: Tyrosine phenol-lyase
B: Tyrosine phenol-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,19716
Polymers205,5104
Non-polymers2,68712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545x,-y-1,-z1
Buried area21250 Å2
ΔGint-72 kcal/mol
Surface area56190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.510, 133.330, 142.840
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 12 or resid 47...
21(chain B and (resid 2 through 12 or resid 47...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNSERSER(chain A and (resid 2 through 12 or resid 47...AA2 - 121 - 11
12LEULEUMETMET(chain A and (resid 2 through 12 or resid 47...AA47 - 6546 - 64
13GLYGLYSERSER(chain A and (resid 2 through 12 or resid 47...AA67 - 1266 - 11
14ASNASNILEILE(chain A and (resid 2 through 12 or resid 47...AA2 - 4561 - 455
15ASNASNILEILE(chain A and (resid 2 through 12 or resid 47...AA2 - 4561 - 455
16ASPASPCYSCYS(chain A and (resid 2 through 12 or resid 47...AA258 - 268257 - 267
17PROPROLEULEU(chain A and (resid 2 through 12 or resid 47...AA289 - 347288 - 346
18SERSERSERSER(chain A and (resid 2 through 12 or resid 47...AA378377
19LEULEUILEILE(chain A and (resid 2 through 12 or resid 47...AA405 - 424404 - 423
21ASNASNSERSER(chain B and (resid 2 through 12 or resid 47...BB2 - 121 - 11
22LEULEUMETMET(chain B and (resid 2 through 12 or resid 47...BB47 - 6546 - 64
23ASNASNP70P70(chain B and (resid 2 through 12 or resid 47...BB - H2 - 5011
24ASNASNASNASN(chain B and (resid 2 through 12 or resid 47...BB21
25ASNASNP70P70(chain B and (resid 2 through 12 or resid 47...BB - H2 - 5011
26ASNASNP70P70(chain B and (resid 2 through 12 or resid 47...BB - H2 - 5011
27PROPROLEULEU(chain B and (resid 2 through 12 or resid 47...BB289 - 347288 - 346
28SERSERSERSER(chain B and (resid 2 through 12 or resid 47...BB378377
29LEULEUILEILE(chain B and (resid 2 through 12 or resid 47...BB405 - 424404 - 423

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tyrosine phenol-lyase / / Beta-tyrosinase


Mass: 51377.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter freundii (bacteria) / Gene: tpl / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P31013, tyrosine phenol-lyase

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Non-polymers , 6 types, 616 molecules

#2: Chemical ChemComp-P71 / (2E)-2-{[(Z)-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4(1H)-ylidene}methyl]imino}-3-phenylpropanoic acid


Mass: 394.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N2O7P
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: K
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330 / Polyethylene glycol


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#6: Chemical ChemComp-P70 / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-phenylalanine


Mass: 394.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19N2O7P
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 610 / 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: 55.28 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M triethanolamine-HCl, pH 8.0, 1 mM EDTA, 5 mM 2-mercaptoethanol, 0.1 mM PLP, 36-38% PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.734 Å / Num. obs: 104987 / % possible obs: 99 % / Redundancy: 13.396 % / Biso Wilson estimate: 33.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.129 / Χ2: 1 / Net I/σ(I): 11.92 / Num. measured all: 1406378 / Scaling rejects: 2194
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.857.733.7560.5154843773970950.2694.02591.7
1.85-1.98.8932.7510.7665058753873160.4132.92197.1
1.9-1.9510.9632.2271.0980000734972970.6092.33699.3
1.95-2.0113.3471.6491.6795562716171600.7421.715100
2.01-2.0814.7931.2162.44102574693669340.8331.26100
2.08-2.1514.8860.9243.2599841671167070.90.95799.9
2.15-2.2314.9040.6974.3596486647864740.940.72199.9
2.23-2.3214.820.555.5392637626262510.9550.56999.8
2.32-2.4314.8890.4137.1889125599759860.9790.42899.8
2.43-2.5514.9190.3388.6685592575257370.9860.34999.7
2.55-2.6814.8560.25611.2580920546554470.990.26599.7
2.68-2.8514.8590.19314.177089520551880.9950.299.7
2.85-3.0414.7970.14218.7772000488848660.9970.14799.5
3.04-3.2914.6510.10523.8766823457445610.9980.10999.7
3.29-3.614.3350.07830.2460036419941880.9980.08199.7
3.6-4.0213.9210.06336.8453192383438210.9990.06599.7
4.02-4.6513.7850.05541.347075342434150.9990.05799.7
4.65-5.6913.7150.05242.7139595289428870.9990.05499.8
5.69-8.0513.5370.04943.4631202230623050.9990.051100
8.05-48.73412.3730.04345.8116728136413520.9990.04599.1

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Processing

Software
NameVersionClassification
PHENIX1.14_3211refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VLF

2vlf


Resolution: 1.8→48.734 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 1992 1.91 %
Rwork0.172 102567 -
obs0.1724 104559 98.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.46 Å2 / Biso mean: 45.4778 Å2 / Biso min: 21.45 Å2
Refinement stepCycle: final / Resolution: 1.8→48.734 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7188 0 88 610 7886
Biso mean--60.64 53.81 -
Num. residues----907
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3052X-RAY DIFFRACTION5.212TORSIONAL
12B3052X-RAY DIFFRACTION5.212TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8450.37591260.35156427655388
1.845-1.89490.31391450.32037021716696
1.8949-1.95070.34161370.30547270740799
1.9507-2.01360.31171330.257173467479100
2.0136-2.08560.2851490.226273767525100
2.0856-2.16910.21291400.199773687508100
2.1691-2.26780.25481500.194573657515100
2.2678-2.38740.21741430.176373867529100
2.3874-2.5370.20071430.175273397482100
2.537-2.73280.19341390.165874147553100
2.7328-3.00780.21471490.169274327581100
3.0078-3.44290.20221350.163174537588100
3.4429-4.33730.15821470.136175567703100
4.3373-48.75150.14671560.153478147970100
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)
10.71880.1665-0.34190.8049-0.19291.32670.09530.20410.2926-0.0585-0.0020.1474-0.257-0.2016-0.05780.28190.07680.02480.27440.05920.325380.3621-45.9636-11.8573
22.59561.67120.91115.68631.59574.47120.08630.26150.4934-0.09270.0453-0.1495-0.66250.2175-0.09090.408-0.02990.10170.32680.13680.44598.2396-28.2061-15.8673
31.09720.19470.06760.9933-0.17222.01760.05440.22820.3194-0.1111-0.0029-0.0356-0.28810.05820.1140.25190.03380.04530.22680.07860.293188.6319-43.2978-15.6612
43.529-1.5529-1.02280.71160.8244.96180.4342-0.03830.6747-0.2963-0.2724-0.2407-1.0058-0.4118-0.19990.54070.15410.05410.53180.1640.543570.6191-36.0882-21.2474
51.5999-1.16641.43045.2265-2.3115.0687-0.02280.55070.2018-0.38110.17210.58520.0486-0.3881-0.09910.27940.0155-0.01490.40730.12070.293875.3385-50.3255-27.363
63.9162-1.0202-0.251.55-1.75943.88950.49910.46690.70390.02550.20810.2895-0.7954-0.9616-0.50970.53270.19490.11040.76060.23690.735362.8557-35.6754-19.3184
72.36281.340.88382.70370.63581.89720.0426-0.119-0.04340.17650.0652-0.24980.01780.2476-0.11850.28190.00530.00420.3308-0.03860.230691.8508-59.97819.9572
83.9215-1.1553-1.20431.65710.38066.32410.10480.10730.1868-0.0609-0.12250.266-0.1792-0.61330.01010.1735-0.0072-0.02030.2829-0.02330.33369.2125-55.31480.7175
90.83760.006-0.03191.59130.50191.85780.0824-0.22770.32940.0431-0.130.2585-0.4469-0.445-0.01540.3440.120.05070.4248-0.11250.450168.8908-40.487917.2616
102.18480.73970.39881.92720.85672.38420.004-0.35810.3270.24060.0088-0.0927-0.19820.1963-0.03190.3639-0.01560.00040.334-0.08310.273290.54-49.332929.8293
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 159 )A2 - 159
2X-RAY DIFFRACTION2chain 'A' and (resid 160 through 207 )A160 - 207
3X-RAY DIFFRACTION3chain 'A' and (resid 208 through 361 )A208 - 361
4X-RAY DIFFRACTION4chain 'A' and (resid 362 through 401 )A362 - 401
5X-RAY DIFFRACTION5chain 'A' and (resid 402 through 429 )A402 - 429
6X-RAY DIFFRACTION6chain 'A' and (resid 430 through 456 )A430 - 456
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 57 )B2 - 57
8X-RAY DIFFRACTION8chain 'B' and (resid 58 through 88 )B58 - 88
9X-RAY DIFFRACTION9chain 'B' and (resid 89 through 311 )B89 - 311
10X-RAY DIFFRACTION10chain 'B' and (resid 312 through 456 )B312 - 456

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