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- PDB-7k4p: Crystal structure of Kemp Eliminase HG3 -

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Basic information

Entry
Database: PDB / ID: 7k4p
TitleCrystal structure of Kemp Eliminase HG3
ComponentsEndo-1,4-beta-xylanase
KeywordsHYDROLASE / kemp elimination / directed evolution
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / xylan catabolic process
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Endo-1,4-beta-xylanase
Similarity search - Component
Biological speciesThermoascus aurantiacus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsPadua, R.A.P. / Otten, R. / Bunzel, A. / Nguyen, V. / Pitsawong, W. / Patterson, M. / Sui, S. / Perry, S.L. / Cohen, A.E. / Hilvert, D. / Kern, D.
Funding support United States, Switzerland, 11items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-05ER15699 United States
Damon Runyon Cancer Research FoundationDRG-2114-12 United States
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM124169 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
National Institutes of Health/Office of the DirectorS10OD021832 United States
Swiss National Science Foundation Switzerland
Other government Switzerland
National Science Foundation (NSF, United States)BioXFEL STC (1231306) United States
CitationJournal: Science / Year: 2020
Title: How directed evolution reshapes the energy landscape in an enzyme to boost catalysis.
Authors: Otten, R. / Padua, R.A.P. / Bunzel, H.A. / Nguyen, V. / Pitsawong, W. / Patterson, M. / Sui, S. / Perry, S.L. / Cohen, A.E. / Hilvert, D. / Kern, D.
History
DepositionSep 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-1,4-beta-xylanase
B: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)66,4012
Polymers66,4012
Non-polymers00
Water10,719595
1
A: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)33,2001
Polymers33,2001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-1,4-beta-xylanase


Theoretical massNumber of molelcules
Total (without water)33,2001
Polymers33,2001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.610, 58.030, 81.610
Angle α, β, γ (deg.)90.000, 101.420, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Endo-1,4-beta-xylanase / Xylanase / 1 / 4-beta-D-xylan xylanohydrolase / TAXI


Mass: 33200.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoascus aurantiacus (fungus) / Gene: XYNA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P23360, endo-1,4-beta-xylanase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / Source method: isolated from a natural source / Formula: H2O
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: 1.77 Å3/Da / Density % sol: 30.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium chloride hexahydrate, 0.1 M HEPES, pH 7.5, 25% (w/v) polyethylene glycol (PEG) 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.9537 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.08→32.93 Å / Num. obs: 188303 / % possible obs: 95.18 % / Redundancy: 6.3 % / Biso Wilson estimate: 9.76 Å2 / CC1/2: 0.998 / Net I/σ(I): 6.37
Reflection shellResolution: 1.081→1.12 Å / Redundancy: 6.2 % / Num. unique obs: 18272 / CC1/2: 0.548 / % possible all: 92.71

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIXdev_3965refinement
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bs0

4bs0


Resolution: 1.08→32.93 Å / SU ML: 0.1423 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.9052
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.213 1997 1.06 %
Rwork0.1932 185978 -
obs0.1934 187975 95.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.88 Å2
Refinement stepCycle: LAST / Resolution: 1.08→32.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4510 0 0 595 5105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00645816
X-RAY DIFFRACTIONf_angle_d0.98348025
X-RAY DIFFRACTIONf_chiral_restr0.07061027
X-RAY DIFFRACTIONf_plane_restr0.0086979
X-RAY DIFFRACTIONf_dihedral_angle_d6.141669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.110.37071380.401312822X-RAY DIFFRACTION92.62
1.11-1.140.34751380.367412946X-RAY DIFFRACTION92.77
1.14-1.170.37041380.331512815X-RAY DIFFRACTION92.29
1.17-1.210.35381390.309512809X-RAY DIFFRACTION91.88
1.21-1.250.28351380.284812997X-RAY DIFFRACTION93.77
1.25-1.30.30641460.26313598X-RAY DIFFRACTION97.52
1.3-1.360.25211450.234913480X-RAY DIFFRACTION96.92
1.36-1.430.25451430.212613456X-RAY DIFFRACTION96.54
1.43-1.520.21431430.195213195X-RAY DIFFRACTION94.76
1.52-1.640.19221390.173112995X-RAY DIFFRACTION93.04
1.64-1.810.18511500.159913873X-RAY DIFFRACTION99.18
1.81-2.070.16611480.1513801X-RAY DIFFRACTION98.78
2.07-2.60.17191460.150413546X-RAY DIFFRACTION96.63
2.61-32.930.17221460.157813645X-RAY DIFFRACTION95.81
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)
10.878350638342-0.0904422981798-0.1067611235170.0679150911651-0.08024334291580.3691649459050.0210741064032-0.2532930680090.11302358130.0586159751302-0.06069807888840.117371199431-0.00632664985357-0.0644546573680.008312200409880.0812457046250.000800028504763-0.01016846721490.143535925279-0.01666745851550.135584437510.47143685672226.709627742551.9186922435
20.6662139421480.06398365364980.1419192389370.3558583547670.1093024307070.2451272000680.0113470711078-0.126628541583-0.01926339037220.0375350258349-0.0426357934317-0.034405712834-0.00340204939205-0.007291078642520.01753797509140.0692545105284-0.00231599079377-0.0174886189860.101408838159-0.000414531971010.12190008747117.30929060230.061805611847.651791365
30.881339026189-0.08378796077250.2423256763550.2703442261650.0852810265640.2801967182310.008766895910780.0352659965291-0.0390728075727-0.0204920416875-0.000391624321305-0.04396387533780.005201558354820.0148080294811-0.01587772226020.064783077665-0.00443882471097-0.007098255420960.079475209568-0.002066879315690.11491451260322.258094728126.363265435235.6488753808
41.03397001216-0.0565181892715-0.1326527679340.754581261676-0.146321280060.2369553854380.02473129623380.124946703883-0.0348315233207-0.0437892244523-0.0317310117825-0.00770498711416-0.01915633865590.00370378895397-0.003804476804770.06695205118970.00198481955991-0.01023444432330.0880219162673-0.007324567891970.10772614150410.840193007423.583258720931.0606840327
51.32681356876-0.493639784915-0.0190250293130.6647291423770.05219709105070.36536222656-0.00440975850775-0.02612998555510.1065908240050.01264989178630.00357765489296-0.0248946926846-0.01034018544180.00418675329504-0.005671486919980.062343682481-0.00202022917526-0.009862560522880.0814853549338-0.00152871237150.123030301695-1.8546223781527.838574434938.0158193765
60.299241477462-0.04424062179890.1163363781310.503765475959-0.1095580549850.483227032794-0.0457937760275-0.2490959240480.177747245130.08054818251480.0320515760924-0.110037525655-0.0537915135628-0.0475591379598-0.04457096106020.06145243569520.0122851505735-0.02130785245710.126227525952-0.04916072031360.16829764765-7.7095985730633.822817311849.672712298
70.0471988174259-0.0224319578547-0.02386323896120.00982489895310.01796934738860.0423364432080.0254885374128-0.227224693452-0.07803003002010.008379212441350.01229587884840.1100875534190.0288878071845-0.1507794137550.001710741519470.0824851365197-0.0305927356709-0.01678334112770.1774420376090.0283749133070.157531059526-20.297119352524.58046662518.81397271722
80.03245717782320.022061755253-0.003141262288050.422882323208-0.1444894800230.1090997137540.046476630643-0.4452193128430.004131316657-0.0587843684289-0.0516907770833-0.0136437058806-0.0183260504518-0.0474399133133-0.02304807823260.0694070817541-0.01733888825120.003862085860410.231735601062-0.03440598684360.1248389092-11.05286346533.808861323514.5290625447
90.418097260694-0.2602856803280.3357180025620.129514016999-0.1091920264110.3225116725840.00474248348315-0.0803638801992-0.023824528764-0.00284961784181-0.00791643129315-0.00737498130917-0.02453597182080.06497361884510.002818971702680.0637234858345-0.00918443078544-0.01078138669720.1197521742860.0101499450150.101259443314.0187994551133.86588528856.02220667263
100.178605784826-0.09005692364270.05922808883620.1815850029080.1209493403830.1955034812660.05752165581950.0616590621881-0.0373029566772-0.0292164422055-0.0342986446308-0.007396161336270.01540292803090.1151918612451.91876312147E-50.06648365414020.00237217711753-0.01104874757210.1248970675910.008724622290880.09705362198314.7630554507329.508771925-4.34750465179
110.1717150727610.141672262697-0.07989126776990.1756719183820.1055006214410.1603940382320.04521699473360.0834054553926-0.0545309524558-0.0361991235607-0.04593480185350.00243542222551-0.004615858914610.03612768016260.002890217560650.07764461316180.00745390935753-0.02125176364610.113000654064-0.006248034200310.117644399416-1.337710645225.5098001184-5.93149007411
120.07730961708020.106822789984-0.1287266679710.12044024738-0.1786414493570.157417655580.08067248406840.110654502169-0.0342570925442-0.0931608284355-0.04377614652380.0918869794553-0.0373227335684-0.008878094623050.003230475018220.1113270686220.0291679261027-0.03521872774220.111744541467-0.01638833990520.12403834248-8.8648448801427.8783047032-11.9467722505
130.143560760325-0.0330977585851-0.04132316713730.0962418687308-0.0623612537430.155507131990.04593704603650.030073413453-0.0111157166854-0.0330628059921-0.01379690246320.05635487459610.0175739279764-0.07943694025080.01479881865320.07569319806870.0170084211784-0.01995044612320.121254398455-0.01531771208460.130229128421-19.889524439630.4111204323-4.32329932496
140.282583161307-0.1261588940680.2108298234550.102462194926-0.06120233922170.195879412381-0.00998834931575-0.1957348379070.05289575175830.05369766631160.0129895970952-0.0352743110827-0.00480022102235-0.1329504547620.0007604220595980.06793275203870.0070347319819-0.0125850059820.159217172957-0.04062300748330.144170376731-21.5046993734.4851998216.8373149601
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 31 )AA1 - 311 - 31
22chain 'A' and (resid 32 through 100 )AA32 - 10032 - 100
33chain 'A' and (resid 101 through 149 )AA101 - 149101 - 149
44chain 'A' and (resid 150 through 213 )AA150 - 213150 - 213
55chain 'A' and (resid 214 through 273 )AA214 - 273214 - 273
66chain 'A' and (resid 274 through 303 )AA274 - 303274 - 299
77chain 'B' and (resid 4 through 22 )BB4 - 221 - 19
88chain 'B' and (resid 23 through 45 )BB23 - 4520 - 42
99chain 'B' and (resid 46 through 100 )BB46 - 10043 - 97
1010chain 'B' and (resid 101 through 149 )BB101 - 14998 - 146
1111chain 'B' and (resid 150 through 180 )BB150 - 180147 - 174
1212chain 'B' and (resid 181 through 213 )BB181 - 213175 - 207
1313chain 'B' and (resid 214 through 256 )BB214 - 256208 - 250
1414chain 'B' and (resid 257 through 303 )BB257 - 303251 - 294

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