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- PDB-5g3o: Bacillus cereus formamidase (BceAmiF) inhibited with urea. -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5g3o
TitleBacillus cereus formamidase (BceAmiF) inhibited with urea.
ComponentsFORMAMIDASE
KeywordsHYDROLASE / FORMAMIDASE / AMIDASE / NITRILASE SUPERFAMILY
Function / homology
Function and homology information


formamidase / formamidase activity / N-carbamoylputrescine amidase activity / putrescine biosynthetic process from arginine / :
Similarity search - Function
Formamidase / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Formamidase / Formamidase
Similarity search - Component
Biological speciesBACILLUS CEREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGavira, J.A. / Martinez-Rodriguez, S. / Conejero-Muriel, M.
CitationJournal: Arch.Biochem.Biophys. / Year: 2019
Title: A novel cysteine carbamoyl-switch is responsible for the inhibition of formamidase, a nitrilase superfamily member.
Authors: Martinez-Rodriguez, S. / Conejero-Muriel, M. / Gavira, J.A.
History
DepositionApr 29, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Mar 6, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _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 / _citation.year
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FORMAMIDASE
B: FORMAMIDASE
C: FORMAMIDASE
D: FORMAMIDASE
E: FORMAMIDASE
F: FORMAMIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,64435
Polymers232,3016
Non-polymers3,34429
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27670 Å2
ΔGint-179.4 kcal/mol
Surface area67130 Å2
MethodPQS
Unit cell
Length a, b, c (Å)142.689, 149.754, 97.220
Angle α, β, γ (deg.)90.00, 98.68, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-2008-

HOH

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
FORMAMIDASE / BCEAMIF / FORMAMIDE AMIDOHYDROLASE


Mass: 38716.750 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: UREA BOUNDED AT CYSTEINE 165, IN ALL THE CHAINS. / Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Plasmid: PET21B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria)
References: UniProt: E5LR94, UniProt: P59701*PLUS, formamidase

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Non-polymers , 5 types, 444 molecules

#2: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.25 Å3/Da / Density % sol: 45.41 % / Description: NONE
Crystal growMethod: counter-diffusion / pH: 4
Details: CAPILLARY COUNTER DIFFUSION: 20% PEG 400, 15% PEG 4K, 10% PEG 8K, NAAC 0.1M PH 4.0 SOAKED WITH 250 MM UREA

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Apr 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→45.48 Å / Num. obs: 108536 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 40.08 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 18.3
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.55 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5G3P
Resolution: 2.15→47.058 Å / SU ML: 0.21 / σ(F): 1.35 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2021 5441 5 %
Rwork0.1786 --
obs0.1793 108523 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.41 Å2
Refinement stepCycle: LAST / Resolution: 2.15→47.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13021 0 219 415 13655
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314687
X-RAY DIFFRACTIONf_angle_d0.62520019
X-RAY DIFFRACTIONf_dihedral_angle_d15.2068822
X-RAY DIFFRACTIONf_chiral_restr0.0482086
X-RAY DIFFRACTIONf_plane_restr0.0052630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.17440.26011790.23413423X-RAY DIFFRACTION100
2.1744-2.20.26761720.2383526X-RAY DIFFRACTION100
2.2-2.22680.26441590.22813402X-RAY DIFFRACTION100
2.2268-2.2550.26491940.23013442X-RAY DIFFRACTION100
2.255-2.28470.26411760.22453421X-RAY DIFFRACTION99
2.2847-2.3160.24021710.20853468X-RAY DIFFRACTION99
2.316-2.34910.23271760.20323399X-RAY DIFFRACTION99
2.3491-2.38410.2631840.20723398X-RAY DIFFRACTION99
2.3841-2.42140.21411530.19753433X-RAY DIFFRACTION99
2.4214-2.46110.20551900.19723447X-RAY DIFFRACTION100
2.4611-2.50350.21581880.1933436X-RAY DIFFRACTION100
2.5035-2.54910.20361920.18423428X-RAY DIFFRACTION100
2.5491-2.59810.2111900.18223437X-RAY DIFFRACTION100
2.5981-2.65110.22581930.18273456X-RAY DIFFRACTION100
2.6511-2.70870.21942140.18313402X-RAY DIFFRACTION100
2.7087-2.77180.21931820.17693452X-RAY DIFFRACTION100
2.7718-2.84110.20871760.173441X-RAY DIFFRACTION100
2.8411-2.91790.19431860.17313454X-RAY DIFFRACTION100
2.9179-3.00370.18591750.17393422X-RAY DIFFRACTION99
3.0037-3.10060.19192000.17453412X-RAY DIFFRACTION99
3.1006-3.21140.21131900.17713412X-RAY DIFFRACTION99
3.2114-3.340.19821950.17183479X-RAY DIFFRACTION100
3.34-3.49190.19151670.16433449X-RAY DIFFRACTION99
3.4919-3.6760.1981970.15473410X-RAY DIFFRACTION99
3.676-3.90620.17711690.1523466X-RAY DIFFRACTION99
3.9062-4.20760.16861690.15543438X-RAY DIFFRACTION99
4.2076-4.63070.15561810.13773403X-RAY DIFFRACTION98
4.6307-5.30.15781790.14733423X-RAY DIFFRACTION99
5.3-6.67440.19751670.18563476X-RAY DIFFRACTION99
6.6744-47.06930.22011770.19233427X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.86360.15030.02292.66810.09952.5520.15830.03870.1915-0.0196-0.2546-0.3219-0.08380.0952-0.01920.2485-0.07420.00840.2686-0.02940.218840.26846.417649.1718
24.598-3.88271.12435.8711-0.49771.50870.2268-0.440.39780.0189-0.0567-0.7222-0.03320.2262-0.0190.3699-0.08480.00070.4488-0.02210.339445.45527.042957.7387
32.2289-0.19860.33742.5624-0.26791.50020.1125-0.2535-0.27240.2193-0.0683-0.07470.15350.0668-0.03170.3106-0.0861-0.01960.35030.04690.301938.7507-3.806554.6237
42.19220.50260.65921.3507-0.1490.590.0823-0.0124-0.23070.0239-0.00810.05180.201-0.0815-0.04290.3371-0.0630.0020.358-0.01060.363829.1847-3.349642.3267
53.4686-0.01450.06740.5598-0.32610.66910.0169-0.0050.1662-0.0121-0.02510.15880.0403-0.10860.00670.3259-0.0342-0.00010.3301-0.03270.353431.10197.225140.9317
64.3677-2.42820.62338.6410.58154.69310.3046-0.0489-1.0006-0.5208-0.04570.18680.81280.1901-0.20080.5081-0.0951-0.0180.41570.12830.471818.5051-19.330635.58
72.54580.20930.20273.01130.42732.10840.02340.78970.0881-0.41690.04570.1579-0.0201-0.1102-0.0740.4150.0718-0.02360.58120.07380.322126.602820.7234-10.4299
84.41110.28720.47935.57661.85243.33220.10510.8223-0.3378-0.09660.0016-0.27480.05410.4031-0.13160.3430.08350.05740.61160.02530.345238.873217.0194-9.3402
92.28131.1610.41930.52120.43020.63010.09560.0880.0323-0.0359-0.0791-0.08540.01380.0963-0.02190.34290.05730.02320.41850.03870.367737.22817.44554.8156
107.872-5.1666-3.28075.32341.75336.7069-0.21580.7888-0.8346-0.42870.1416-0.41560.39261.05470.0690.38630.00260.1010.63640.03110.334960.61257.3893-3.1215
111.5838-0.2797-0.92142.7646-1.29941.73510.041-0.46790.1958-0.0503-0.26310.2319-0.06460.03840.24680.30.06440.0290.31620.03350.2458.30754.047628.9192
125.12875.13321.71065.34840.75163.36750.2007-0.57730.03490.7321-0.3701-0.15090.06790.61240.25470.39260.0922-0.00880.45410.05410.367265.47980.820834.8129
131.94441.6081-0.40812.0571-0.77111.06480.1605-0.2320.15440.0948-0.25880.23690.11660.298-0.03850.35790.08990.03470.39240.01710.335860.22172.650527.0073
143.92541.0505-0.18696.1136-0.50012.06810.1402-0.20660.46410.2993-0.1732-0.5877-0.05770.6495-0.03270.38990.01110.02960.55410.02430.420174.8913.213325.3412
153.33611.8739-0.3552.8593-0.39281.77530.0601-0.1837-0.4670.0046-0.1553-0.52560.35570.48640.10040.36570.10780.04950.46880.01960.388667.3276-4.296125.9645
163.83931.754-0.99363.2043-0.63792.2824-0.10210.26420.2767-0.17710.1013-0.2227-0.11180.66230.0620.33690.06580.05920.57810.01280.388873.60897.675216.9109
172.62410.96070.30674.6727-2.12933.5786-0.138-0.0080.2302-0.1724-0.0329-0.3803-0.2260.26890.24870.33650.07410.02010.4985-0.02510.307365.45377.310516.4233
182.49632.5507-0.86356.0941-1.46632.3839-0.00140.3715-0.4087-0.2376-0.0314-0.32720.32710.40440.21970.40920.11710.06560.492-0.00520.333862.3120.578712.2508
191.78470.84910.33960.44520.07691.1956-0.11820.21340.0618-0.2280.1822-0.1218-0.10750.2648-0.0480.40060.08730.03950.4512-0.00610.349656.13957.750312.0275
202.62290.87761.23797.39775.25333.8771-0.06240.11080.26040.3536-0.00340.04730.2407-0.04340.03060.37970.0490.04130.39530.01070.355846.923811.805415.687
211.1252-0.23390.41560.98530.75542.17210.02950.1501-0.0283-0.1757-0.12550.00890.1645-0.05710.0830.31120.02180.04920.3490.02280.282349.41376.352624.0738
224.31614.4172-3.7725.1296-5.83499.0053-0.3280.5101-0.0469-0.4380.24-0.33440.2516-0.09880.0320.30660.13390.10740.5059-0.09220.40953.01195.7535-1.5948
232.126-0.0692-0.45491.52770.15652.741-0.0699-0.18950.41130.18950.0435-0.3622-0.25030.23570.00780.3078-0.0159-0.04110.2581-0.0280.464452.58936.162842.0606
244.4647-2.34040.8851.37070.04052.261-0.403-0.4984-0.20030.4070.52140.3372-0.4208-0.8434-0.14910.46540.01230.02230.4682-0.05120.48335.742137.750646.9724
251.0093-1.01441.08751.6196-0.59921.15730.04470.01950.2227-0.0741-0.1164-0.0603-0.1308-0.02560.08550.31950.00780.01250.30130.00020.420138.869831.296431.0749
268.8025-1.7877-1.164.54421.16260.353-0.2432-0.81070.633-0.00710.12030.4109-0.7194-0.75-0.03980.51630.0637-0.07420.3174-0.08020.483917.774847.03434.2185
271.28580.31650.5042.1013-0.88562.5066-0.0658-0.05850.1442-0.0769-0.07410.4757-0.2083-0.39120.09760.30740.0337-0.04950.4323-0.08230.47531.170326.06517.4588
283.50820.7470.36635.5573-0.88726.1289-0.13250.02570.62250.0014-0.05830.1377-0.92150.0650.26690.35970.1184-0.08790.3237-0.07750.43356.302638.788221.9825
290.6199-0.43760.71861.21950.462.4235-0.0446-0.08250.1480.0758-0.04830.0666-0.0791-0.08180.09780.29980.0074-0.01740.3292-0.05720.386217.011825.823827.4301
304.6904-0.35241.10112.1579-2.52266.2644-0.1486-0.35890.55480.2827-0.07310.1125-0.6773-0.0250.22560.57810.08040.03040.4208-0.12520.450125.57746.956837.714
311.46371.7539-1.10743.32770.48713.7185-0.31760.0430.72660.00990.2164-0.03890.1378-0.17910.05350.4322-0.0049-0.10720.2882-0.03840.248615.5538-2.58599.2318
328.7786-0.7704-1.86751.08450.1483.16230.05530.61940.4611-0.37930.07220.23760.0838-0.3667-0.18830.57940.0027-0.12530.4618-0.04410.40410.2061-5.28021.2388
333.84220.1624-0.48281.4308-0.35452.70750.17290.1518-0.3257-0.25890.04790.18680.4496-0.3655-0.15080.4777-0.0699-0.15180.36920.01290.37268.863-10.01528.9077
346.7472-2.0116-2.50092.57480.25966.10640.121-0.0523-0.7567-0.1059-0.07720.330.5813-0.38840.04130.5439-0.1279-0.20250.2988-0.00670.4669.3104-17.820914.5644
358.8104-1.8053-1.32553.4268-1.01416.2386-0.2711-1.1340.1510.7260.59870.3753-0.1505-0.782-0.34270.4517-0.0002-0.09440.6033-0.00280.41367.0238-9.431426.009
361.4985-0.86670.7261.5602-0.99690.42190.065-0.008-0.0351-0.0866-0.0170.02630.1874-0.0759-0.01240.4069-0.0078-0.05050.3429-0.01620.341321.34-3.674821.0465
372.3632-1.22850.62212.8872-1.03781.37310.31220.2687-0.0764-0.4193-0.3401-0.22740.51380.10560.09420.4680.0338-0.00230.43450.00080.45334.2741-11.646116.2223
389.32640.3584-4.0375.6861-0.55162.30870.1059-0.5526-0.40950.97270.15810.08420.4750.0804-0.24460.5945-0.108-0.15820.46680.05570.546321.253-16.831841.9637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 12 THROUGH 28 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 29 THROUGH 49 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 50 THROUGH 141 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 142 THROUGH 210 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 211 THROUGH 267 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 268 THROUGH 308 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 12 THROUGH 120 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 121 THROUGH 163 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 164 THROUGH 267 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 268 THROUGH 307 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 12 THROUGH 28 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 29 THROUGH 49 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 50 THROUGH 67 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 68 THROUGH 82 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 83 THROUGH 105 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 106 THROUGH 120 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 121 THROUGH 141 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 142 THROUGH 163 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 164 THROUGH 192 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 193 THROUGH 210 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 211 THROUGH 258 )
22X-RAY DIFFRACTION22CHAIN 'C' AND (RESID 259 THROUGH 307 )
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 12 THROUGH 131 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 132 THROUGH 151 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 152 THROUGH 267 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 268 THROUGH 307 )
27X-RAY DIFFRACTION27CHAIN 'E' AND (RESID 12 THROUGH 105 )
28X-RAY DIFFRACTION28CHAIN 'E' AND (RESID 106 THROUGH 151 )
29X-RAY DIFFRACTION29CHAIN 'E' AND (RESID 152 THROUGH 268 )
30X-RAY DIFFRACTION30CHAIN 'E' AND (RESID 269 THROUGH 307 )
31X-RAY DIFFRACTION31CHAIN 'F' AND (RESID 12 THROUGH 28 )
32X-RAY DIFFRACTION32CHAIN 'F' AND (RESID 29 THROUGH 49 )
33X-RAY DIFFRACTION33CHAIN 'F' AND (RESID 50 THROUGH 105 )
34X-RAY DIFFRACTION34CHAIN 'F' AND (RESID 106 THROUGH 131 )
35X-RAY DIFFRACTION35CHAIN 'F' AND (RESID 132 THROUGH 151 )
36X-RAY DIFFRACTION36CHAIN 'F' AND (RESID 152 THROUGH 251 )
37X-RAY DIFFRACTION37CHAIN 'F' AND (RESID 252 THROUGH 267 )
38X-RAY DIFFRACTION38CHAIN 'F' AND (RESID 268 THROUGH 307 )

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