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- PDB-9ms4: Crystal structure of an expansin (Xa_EXLX1) from Xanthomonas sacchari -

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Basic information

Entry
Database: PDB / ID: 9ms4
TitleCrystal structure of an expansin (Xa_EXLX1) from Xanthomonas sacchari
ComponentsExpansin (Peptidoglycan-binding protein)
KeywordsSUGAR BINDING PROTEIN / bacterial expansin / carbohydrate-binding / cellulose-loosening
Function / homology: / : / Expansin, cellulose-binding-like domain superfamily / RlpA-like domain superfamily / : / Expansin (Peptidoglycan-binding protein)
Function and homology information
Biological speciesXanthomonas sacchari (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSmith, C.A. / Buchko, G.W. / Momeni, M.H. / Master, E.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Insights into the action of phylogenetically diverse microbial expansins
Authors: Buchko, G.W. / Smith, C.A. / Momeni, M.H. / Master, E.R.
History
DepositionJan 9, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Expansin (Peptidoglycan-binding protein)
B: Expansin (Peptidoglycan-binding protein)
C: Expansin (Peptidoglycan-binding protein)
D: Expansin (Peptidoglycan-binding protein)
E: Expansin (Peptidoglycan-binding protein)
F: Expansin (Peptidoglycan-binding protein)
G: Expansin (Peptidoglycan-binding protein)
H: Expansin (Peptidoglycan-binding protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,96618
Polymers179,6828
Non-polymers1,28510
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)201.205, 47.884, 201.435
Angle α, β, γ (deg.)90.00, 90.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Expansin (Peptidoglycan-binding protein) / Xs_EXLX1


Mass: 22460.193 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas sacchari (bacteria) / Gene: FHR56_002727 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7X0FIU8
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-A1BNY / 2-hydroxy-3,5-dinitrobenzoic acid / 3,5-Dinitrosalicylic acid / DNS / DNSA


Mass: 228.116 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H4N2O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.05 M Hepes pH 6.8, PEG 4000, silver bullet #1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.3→90.11 Å / Num. obs: 85530 / % possible obs: 99 % / Redundancy: 7 % / CC1/2: 0.994 / Rpim(I) all: 0.092 / Rrim(I) all: 0.178 / Net I/σ(I): 7.2
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 4196 / CC1/2: 0.572 / Rpim(I) all: 0.783

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Processing

Software
NameVersionClassification
PHENIX(1.21.2_5419: ???)refinement
autoPROCdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→90.11 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2398 4433 5.19 %
Rwork0.1882 --
obs0.1908 85430 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→90.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12644 0 88 262 12994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813038
X-RAY DIFFRACTIONf_angle_d0.93217804
X-RAY DIFFRACTIONf_dihedral_angle_d16.0884598
X-RAY DIFFRACTIONf_chiral_restr0.0551944
X-RAY DIFFRACTIONf_plane_restr0.0072344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.330.34511400.29252608X-RAY DIFFRACTION98
2.33-2.350.35641400.29112726X-RAY DIFFRACTION100
2.35-2.380.35071410.28052691X-RAY DIFFRACTION99
2.38-2.410.32941440.27372693X-RAY DIFFRACTION100
2.41-2.450.32431470.27692653X-RAY DIFFRACTION100
2.45-2.480.37411380.27932733X-RAY DIFFRACTION99
2.48-2.510.31481440.26162723X-RAY DIFFRACTION100
2.51-2.550.29941510.25722633X-RAY DIFFRACTION100
2.55-2.590.32491440.25412700X-RAY DIFFRACTION100
2.59-2.630.32131560.23422715X-RAY DIFFRACTION100
2.63-2.680.27151460.21472707X-RAY DIFFRACTION99
2.68-2.730.28341430.22552692X-RAY DIFFRACTION100
2.73-2.780.29791600.22552675X-RAY DIFFRACTION100
2.78-2.840.30171440.22632666X-RAY DIFFRACTION97
2.84-2.90.28781360.22472542X-RAY DIFFRACTION95
2.9-2.970.2571780.22262712X-RAY DIFFRACTION99
2.97-3.040.27141170.22082714X-RAY DIFFRACTION100
3.04-3.120.27861430.21832707X-RAY DIFFRACTION100
3.12-3.210.281590.20442723X-RAY DIFFRACTION100
3.21-3.320.28281750.21652678X-RAY DIFFRACTION100
3.32-3.440.25011230.19732790X-RAY DIFFRACTION99
3.44-3.570.26371240.18862699X-RAY DIFFRACTION100
3.57-3.740.20791760.18272707X-RAY DIFFRACTION99
3.74-3.930.19641380.16192725X-RAY DIFFRACTION99
3.93-4.180.18991330.14392651X-RAY DIFFRACTION97
4.18-4.50.1681710.13412651X-RAY DIFFRACTION97
4.5-4.960.18751460.13822763X-RAY DIFFRACTION100
4.96-5.670.18841290.14432790X-RAY DIFFRACTION100
5.68-7.150.21341710.16152781X-RAY DIFFRACTION100
7.15-90.110.20241760.14862749X-RAY DIFFRACTION94
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)
1-0.0326-0.20570.05820.9763-0.40682.0118-0.0204-0.111-0.3849-0.1080.06670.02410.0434-0.25070.00070.3763-0.0103-0.01540.55910.03330.4571-13.337329.486689.1633
21.3635-1.19240.33021.07630.16341.6963-0.1584-0.19090.03590.15090.15970.37650.1651-0.1453-0.00030.5042-0.0317-0.00450.45090.02230.4176-13.11526.526986.8489
30.60010.0339-0.63990.3527-0.19560.59220.1013-0.3280.15350.3972-0.11580.33140.0675-0.16940.00020.50520.05050.02980.53340.04190.5253-14.907830.49487.9143
40.3510.3152-0.07510.5859-0.25660.6503-0.2626-0.28830.0230.56780.33190.29120.0165-0.56810.00010.55240.11850.04660.72420.06610.4826-18.395730.382296.0608
50.7167-0.03720.75911.1683-0.10650.66790.0550.0363-0.04790.0844-0.0553-0.22270.09710.0162-0.00010.4454-0.0269-0.0520.4170.00450.4759-5.83917.456973.4397
60.4575-0.05370.43790.62310.40370.6050.00680.2050.3023-0.33090.0445-0.4299-0.1641-0.0015-0.00010.5415-0.05320.02150.4515-0.00880.4914-1.151121.316466.8436
71.4886-0.4838-0.00991.51490.53010.21960.14020.3283-0.0682-0.12770.032-0.30030.31560.49370.00150.46140.0129-0.01660.3650.0030.4243-2.204315.219470.8906
80.73160.1175-0.21980.536-0.24750.1244-0.03750.1628-0.12650.26610.3435-0.16070.21240.04320.0010.39990.0348-0.14120.41170.05210.5222-5.307310.629778.5014
90.51440.85990.29111.2657-0.07031.8961-0.10910.29560.0941-0.0385-0.1132-0.1392-0.00190.2369-0.00020.3423-0.0445-0.02170.49430.04490.388315.309650.844312.9888
101.50.06860.94450.497-0.35440.80520.04990.39620.0776-0.04220.0301-0.0928-0.161-0.0472-0.00010.3467-0.04080.00240.36790.04070.38599.997451.29310.9969
110.2477-0.0317-0.4460.4686-0.01770.70340.22960.17380.2102-0.1247-0.1069-0.5072-0.17590.2351-0.00020.4133-0.0673-0.07240.55140.01020.481715.299153.862712.0589
120.37-0.59810.43790.8575-0.75670.53750.04040.16690.2932-0.59620.087-0.0859-0.11150.2856-00.3995-0.05550.0150.53080.00590.440818.360753.74993.7266
130.5838-0.86090.75691.4249-0.77720.8277-0.03570.00460.07040.1192-0.1550.0193-0.20160.2824-0.00020.3732-0.0566-0.01520.36320.00360.42546.982340.923727.0042
141.277-0.01221.32970.8199-0.05711.5663-0.0416-0.0024-0.040.2150.10160.2225-0.09510.0032-0.00020.3493-0.0415-0.00820.39530.02980.41353.10241.654831.6599
150.5181-0.1115-0.10630.5582-0.17550.08730.19760.1636-1.28570.12650.50610.3473-0.42640.44420.01120.3795-0.0447-0.05780.4149-0.01810.53886.059534.053821.9585
161.4810.38910.42360.8249-0.13920.1744-0.14860.20410.1045-0.06650.23350.10780.1585-0.1021-0.00010.4565-0.00530.01560.56490.03340.4421-38.315441.007636.8509
170.9076-0.11340.47241.5241-1.25780.8445-0.22770.1748-0.1893-0.09260.14540.27310.0928-0.031800.460.0096-0.00880.4226-0.03870.4217-35.982138.041337.0077
180.72510.15120.59180.3368-0.05640.41720.15210.35370.2656-0.7188-0.11190.1532-0.0171-0.30780.00010.5248-0.0203-0.00920.54530.06110.5517-37.127741.950235.196
191.48820.00820.12630.46320.31620.4533-0.13890.24520.0199-0.13820.29820.62130.0797-0.2843-0.00020.4646-0.0373-0.03580.54850.02830.5453-45.373241.716231.9265
201.1714-1.21040.1121.65020.01711.1110.03120.1597-0.1291-0.0421-0.08030.0177-0.08740.003200.4270.00610.03680.36580.03330.4138-21.421530.638745.3292
210.7363-0.47990.30681.25520.54760.8258-0.1821-0.2994-0.07260.56090.0763-0.2417-0.08870.2619-00.38130.02920.09090.4060.0320.4395-20.721928.551850.8987
220.0351-0.0064-0.06530.00030.02870.1587-0.4344-0.2018-0.11310.03690.1629-0.4752-0.52510.3295-0.00250.5230.06480.10150.4170.06840.4624-8.189726.228638.5266
230.08320.09040.04360.20650.27790.3864-0.6320.7644-0.9134-0.25810.11410.04460.534-0.2039-0.00290.58780.01070.04340.42150.03520.5035-27.388222.269844.893
241.7736-0.1454-0.02020.80110.92880.75110.0118-0.25870.15330.0932-0.05830.11890.19430.24960.00010.4002-0.0715-0.02990.53210.01350.448436.372515.846463.3894
250.638-0.41090.57690.8203-0.37770.3985-0.092-0.2266-0.53440.48050.1241-0.27840.04740.41660.00060.4155-0.0308-0.02430.6107-0.04840.490543.587814.333865.2065
260.67420.47870.40560.34860.30580.2402-0.1918-0.46120.23220.05510.0932-0.645-0.40370.250.00190.5463-0.09660.07950.5742-0.06780.554541.429720.543968.5992
271.0809-0.23690.16110.75330.03070.53310.2219-0.4333-0.09060.182-0.1399-0.24580.1770.0131-00.4415-0.04840.03460.5452-0.00360.429744.937513.883264.4434
280.58970.2179-0.64991.4375-0.42950.66670.1659-0.00690.23280.0429-0.12360.08430.06580.0840.00030.4544-0.0194-0.01350.4204-0.04960.418221.59726.439256.4613
290.28010.393-0.41691.3224-0.38580.61940.0186-0.14160.1014-0.381-0.13840.1179-0.4133-0.0596-0.00030.4551-0.0036-0.04180.4325-0.04260.39517.18549.094152.245
300.5036-0.39890.02310.69650.48880.6205-0.22931.0578-0.2544-0.29740.226-0.29190.2525-0.06370.00040.4661-0.0463-0.02960.41920.00270.356927.30873.328448.4463
310.32310.82560.11362.09950.71891.10460.02770.29750.15660.0418-0.0609-0.20050.2562-0.0713-0.00020.3878-0.0013-0.0130.3631-0.01040.466320.73670.224158.9171
320.9349-0.00991.34741.4204-0.04181.67580.0758-0.1983-0.03590.18220.00490.037-0.34740.1429-00.5961-0.21460.05340.5782-0.05520.450414.127744.777788.1717
330.6960.2355-0.6341.24720.12780.50860.3857-0.33530.06360.00850.0513-0.039-0.16610.4006-0.00050.6944-0.23950.04530.6023-0.04720.491920.373345.242486.4472
340.26290.49150.00390.7769-0.00730.8145-0.04270.13350.09740.5457-0.16230.3647-0.76530.4078-0.00040.7993-0.2120.04730.5929-0.02340.511515.059246.803992.2849
351.2342-0.43550.83410.68-0.84210.91610.0249-0.24690.0120.197-0.22170.141-0.19030.24630.00010.66-0.12940.06720.57280.03560.41614.415840.184983.736
361.4185-0.4585-0.78241.8224-0.55330.53640.07580.00090.0168-0.1386-0.0672-0.06240.02230.188600.4773-0.03880.03480.4952-0.01680.464313.988735.204368.3368
370.7627-0.06141.41341.735-0.30432.53660.04920.2051-0.1989-0.0153-0.065-0.0359-0.6149-0.17940.00020.53940.08270.0080.4722-0.02910.396-13.605320.508413.2304
381.09930.2643-0.45140.825-0.55581.79550.09070.1099-0.0053-0.1156-0.01350.1025-0.3947-0.3948-0.00010.62860.12220.01390.46680.00810.4474-16.861921.7411.728
390.8245-0.40580.57490.39340.04690.773-0.13940.26650.3168-0.14660.3108-0.1554-0.5936-0.6222-00.76990.12980.03440.62660.00250.5181-20.582724.49994.6731
401.229-1.3047-0.46293.11720.82850.9045-0.0403-0.02640.00660.1401-0.02380.0147-0.0854-0.0792-0.00010.43590.03650.05050.38090.05950.3921-10.717112.482332.5396
410.58410.6972-0.15580.809-0.09730.360.0236-0.72360.09150.36860.0830.06670.0939-0.50710.00030.34480.0590.03410.45670.02990.5913-19.6749.203433.184
420.848-0.584-0.68941.46980.07250.66110.28280.0109-0.44760.2371-0.037-0.14920.150.11270.00030.4235-0.0116-0.02620.36360.02410.4419-7.53175.818830.5617
431.49370.2446-1.33190.1708-0.16211.0980.0454-0.11930.5405-0.03490.0782-0.13130.3116-0.3093-0.00020.4739-0.0648-0.05610.5239-0.06420.6767-37.756111.309365.92
442.7296-0.02990.90121.14830.53630.2907-0.031-0.45050.290.089-0.13360.14230.2705-0.1697-00.5172-0.0440.0250.5237-0.10070.5615-37.49189.275865.6169
450.76280.0450.10110.80080.46650.76030.0327-0.0660.12610.0596-0.19330.30960.1113-0.3001-0.00090.544-0.01940.0630.4883-0.0390.5498-32.25444.411964.195
460.71660.77310.67273.21920.5280.70040.1009-0.0656-0.03060.2385-0.1324-0.2309-0.0196-0.02650.00010.5169-0.01-0.04540.44590.05040.3744-15.71582.262362.8605
471.63670.74760.84482.14030.38891.05670.1041-0.2145-0.11310.2867-0.1837-0.12480.01060.18640.00010.5910.0063-0.02530.37670.05940.4465-18.3208-4.225864.0857
481.7070.1527-0.85222.2041-0.18550.38840.13280.1080.44010.204-0.1546-0.1877-0.26150.14250.00020.4033-0.018-0.02190.50910.07990.5738.126432.154435.8319
490.35550.45380.45111.22050.6750.5382-0.0744-0.29480.5927-0.42510.0620.20410.1750.45610.00030.4961-0.080.01550.53960.12720.490936.142732.572329.6775
500.8977-0.23040.43610.9014-0.39050.2456-0.30120.17750.45840.76640.0477-0.4576-0.06280.1528-0.00020.5036-0.0265-0.07390.49150.11180.664142.152334.220334.7524
510.65530.1272-0.52440.3222-0.08670.5341-0.15270.85160.3754-0.19660.1225-0.4144-0.4416-0.01550.00070.4360.006-0.03320.72510.15920.772546.812836.187528.9492
520.85920.38980.07963.6105-0.59771.17790.17250.2545-0.0508-0.1693-0.20510.1634-0.12730.08690.00020.4196-0.0328-0.0570.4508-0.01590.409120.130324.161237.7962
530.3489-0.2880.5582.24390.08552.7722-0.08330.0431-0.105-0.08970.04960.24160.0835-0.19610.00010.4172-0.0659-0.02890.4083-0.03080.457517.988820.113237.5961
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 92 )
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 109 )
4X-RAY DIFFRACTION4chain 'A' and (resid 110 through 135 )
5X-RAY DIFFRACTION5chain 'A' and (resid 136 through 174 )
6X-RAY DIFFRACTION6chain 'A' and (resid 175 through 198 )
7X-RAY DIFFRACTION7chain 'A' and (resid 199 through 226 )
8X-RAY DIFFRACTION8chain 'A' and (resid 227 through 237 )
9X-RAY DIFFRACTION9chain 'B' and (resid 29 through 71 )
10X-RAY DIFFRACTION10chain 'B' and (resid 72 through 92 )
11X-RAY DIFFRACTION11chain 'B' and (resid 93 through 109 )
12X-RAY DIFFRACTION12chain 'B' and (resid 110 through 135 )
13X-RAY DIFFRACTION13chain 'B' and (resid 136 through 174 )
14X-RAY DIFFRACTION14chain 'B' and (resid 175 through 226 )
15X-RAY DIFFRACTION15chain 'B' and (resid 227 through 237 )
16X-RAY DIFFRACTION16chain 'C' and (resid 29 through 52 )
17X-RAY DIFFRACTION17chain 'C' and (resid 53 through 92 )
18X-RAY DIFFRACTION18chain 'C' and (resid 93 through 109 )
19X-RAY DIFFRACTION19chain 'C' and (resid 110 through 135 )
20X-RAY DIFFRACTION20chain 'C' and (resid 136 through 188 )
21X-RAY DIFFRACTION21chain 'C' and (resid 189 through 215 )
22X-RAY DIFFRACTION22chain 'C' and (resid 216 through 226 )
23X-RAY DIFFRACTION23chain 'C' and (resid 227 through 237 )
24X-RAY DIFFRACTION24chain 'D' and (resid 29 through 83 )
25X-RAY DIFFRACTION25chain 'D' and (resid 84 through 102 )
26X-RAY DIFFRACTION26chain 'D' and (resid 103 through 118 )
27X-RAY DIFFRACTION27chain 'D' and (resid 119 through 143 )
28X-RAY DIFFRACTION28chain 'D' and (resid 144 through 174 )
29X-RAY DIFFRACTION29chain 'D' and (resid 175 through 198 )
30X-RAY DIFFRACTION30chain 'D' and (resid 199 through 215 )
31X-RAY DIFFRACTION31chain 'D' and (resid 216 through 237 )
32X-RAY DIFFRACTION32chain 'E' and (resid 31 through 71 )
33X-RAY DIFFRACTION33chain 'E' and (resid 72 through 92 )
34X-RAY DIFFRACTION34chain 'E' and (resid 93 through 120 )
35X-RAY DIFFRACTION35chain 'E' and (resid 121 through 154 )
36X-RAY DIFFRACTION36chain 'E' and (resid 155 through 237 )
37X-RAY DIFFRACTION37chain 'F' and (resid 31 through 71 )
38X-RAY DIFFRACTION38chain 'F' and (resid 72 through 120 )
39X-RAY DIFFRACTION39chain 'F' and (resid 121 through 135 )
40X-RAY DIFFRACTION40chain 'F' and (resid 136 through 198 )
41X-RAY DIFFRACTION41chain 'F' and (resid 199 through 215 )
42X-RAY DIFFRACTION42chain 'F' and (resid 216 through 237 )
43X-RAY DIFFRACTION43chain 'G' and (resid 31 through 52 )
44X-RAY DIFFRACTION44chain 'G' and (resid 53 through 120 )
45X-RAY DIFFRACTION45chain 'G' and (resid 121 through 154 )
46X-RAY DIFFRACTION46chain 'G' and (resid 155 through 198 )
47X-RAY DIFFRACTION47chain 'G' and (resid 199 through 237 )
48X-RAY DIFFRACTION48chain 'H' and (resid 31 through 71 )
49X-RAY DIFFRACTION49chain 'H' and (resid 72 through 92 )
50X-RAY DIFFRACTION50chain 'H' and (resid 93 through 120 )
51X-RAY DIFFRACTION51chain 'H' and (resid 121 through 135 )
52X-RAY DIFFRACTION52chain 'H' and (resid 136 through 188 )
53X-RAY DIFFRACTION53chain 'H' and (resid 189 through 237 )

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