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- PDB-8rem: CTX-M-14 measured via serial crystallography from a kapton HARE-c... -

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Basic information

Entry
Database: PDB / ID: 8rem
TitleCTX-M-14 measured via serial crystallography from a kapton HARE-chip (50 micron)
ComponentsBeta-lactamase
KeywordsHYDROLASE / Lysozyme / enzyme / muramidase
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsBosman, R. / Prester, A. / von Soosten, L. / Dibenedetto, S. / Bartels, K. / Sung, S. / von Stetten, D. / Mehrabi, P. / Schulz, E.C.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)458246365 Germany
German Research Foundation (DFG)451079909 Germany
German Federal Ministry for Economic Affairs and Energy01KI2114 Germany
Citation
Journal: To Be Published
Title: Kapton-based HARE chips for fixed-target serial crystallography
Authors: Bosman, R. / Prester, A. / von Soosten, L. / Dibenedetto, S. / Bartels, K. / Sung, S. / von Stetten, D. / Mehrabi, P. / Blatter, G. / Lu, G. / Bernhard, S. / Osbild, M. / Schulz, E.C.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Adams, P.D.
History
DepositionDec 11, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8672
Polymers27,7711
Non-polymers961
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-17 kcal/mol
Surface area10680 Å2
Unit cell
Length a, b, c (Å)42.150, 42.150, 234.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Beta-lactamase


Mass: 27771.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: ctx-m-14 / Production host: Escherichia coli (E. coli) / References: UniProt: D2D9A0, beta-lactamase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal growTemperature: 293 K / Method: batch mode
Details: CTX-M-14 solution (22 mg/ml) was mixed with 45% precipitant solution (40% PEG8000, 200mM lithium sulfate, 100mM sodium acetate, pH 4.5) and with 5% undiluted seed stock in batch

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Apr 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.63→78.07 Å / Num. obs: 31622 / % possible obs: 99.99 % / Redundancy: 337.1 % / Biso Wilson estimate: 20.71 Å2 / CC1/2: 0.983 / CC star: 0.996 / R split: 0.0979 / Net I/σ(I): 7.52
Reflection shellResolution: 1.63→1.68 Å / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2673 / CC1/2: 0.686 / CC star: 0.902 / R split: 0.727 / % possible all: 99.93
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrystFEL0.10.2data reduction
CrystFEL0.10.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→78.07 Å / SU ML: 0.1576 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.7888
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1825 1552 4.94 %
Rwork0.1555 29860 -
obs0.1568 31412 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.41 Å2
Refinement stepCycle: LAST / Resolution: 1.63→78.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1941 0 5 165 2111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01062142
X-RAY DIFFRACTIONf_angle_d1.07922941
X-RAY DIFFRACTIONf_chiral_restr0.0647343
X-RAY DIFFRACTIONf_plane_restr0.0099396
X-RAY DIFFRACTIONf_dihedral_angle_d13.6615808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.680.3422960.28482499X-RAY DIFFRACTION92.22
1.68-1.740.29511180.22362689X-RAY DIFFRACTION99.54
1.74-1.810.2521660.21672605X-RAY DIFFRACTION99.71
1.81-1.890.24841520.20092683X-RAY DIFFRACTION99.75
1.89-1.990.1821350.15522721X-RAY DIFFRACTION99.93
1.99-2.120.16021650.14792670X-RAY DIFFRACTION99.93
2.12-2.280.16311430.1482707X-RAY DIFFRACTION99.89
2.28-2.510.16951470.15952725X-RAY DIFFRACTION99.9
2.51-2.870.18861070.15942780X-RAY DIFFRACTION99.93
2.87-3.620.19381600.15032795X-RAY DIFFRACTION100
3.62-78.070.15371630.12892986X-RAY DIFFRACTION99.94
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)
14.17341768864-2.34284235067-1.423340640214.316467809370.8251022193622.33257533023-0.1434029968130.241744120773-0.0873678843669-0.2301234224380.02781467977760.3431155209020.0664075459759-0.942651988450.1267429277240.160683761799-0.00168218352874-0.03410751442280.3002203550790.00924811718610.156355279433-12.6099216339-11.12791917117.17458281373
20.188990265482-0.1079362464710.1281313614872.736956858880.6957063085311.53447404629-0.0198387027973-0.02322724486360.0429870937682-0.0419702384479-0.1041293699370.249084450295-0.222980066731-0.6093453068990.04510756982550.1702227442920.0625232153346-0.000179849777720.2425533749060.0002814971036850.18284344487-11.2256662805-0.74220904480122.1424125612
33.13936457931-1.95368287207-3.440538400062.717459509051.541909968534.99943093135-0.138807429276-0.7439779557830.5696278643190.169409819330.265799658721-0.200012124168-0.9272440393690.160767952249-0.1470576920520.571609201401-0.0021284011720.005138572705410.25084315079-0.0232079840590.26768559492.427555075316.045803297234.4436598695
40.2063930021490.06491165236490.3787975351041.57776247810.3530362852042.88875041818-0.0574317214731-0.02181515282370.125409609474-0.1227938690580.113653520965-0.186596771377-0.7438926494750.101534064973-0.006371415834850.299514980422-0.02282731392660.02918054748970.110627353657-0.006150844140.196101156022.921351103278.787025027327.4822620773
52.88783136513-2.041657782870.408483512393.832043122121.525203013823.96643053910.161935256412-0.0279576925085-0.3053026927970.10447765187-0.0081388799807-0.02701639451010.156005965138-0.111019426816-0.127374493690.135853626949-0.00160645455015-0.02686094741340.08517497900320.01880381385810.150466118261-1.28501788334-7.5789458500127.4315346477
62.21085512024-3.829806598070.416039934537.58194730266-0.844275128981.20019203127-0.02489053453820.0452493435944-0.0921104965393-0.0876394175384-0.09051212374190.365781111792-0.0960573820931-0.7745445026170.04183906878250.1490803568070.0744418084933-0.0202181148440.348485471858-0.01716238825570.192829376065-15.1176979507-1.0759522366322.1998162415
70.805582103788-0.2704095617520.3398995987821.657035271220.7313892551961.50739833468-0.05298664188810.02268343796170.173625171868-0.4983118444340.03423660222240.0913388376606-0.882425275356-0.3295594978240.06447883898630.4716968022690.201169289235-0.03943278147980.1702433099270.03805902374130.182269943199-9.076432282687.1012214945515.4128826993
85.81946430548-1.865231659721.600717858752.43953341966-1.086509036191.12323868482-0.1340841199730.3988045623230.302373835837-0.41505115527-0.2005656293990.214355037893-0.73098649007-0.726829979152-0.1853687636070.3807476627770.282937457867-0.1138914014340.368981203350.00439748482410.251955652561-13.42080098960.24661807266411.7105555176
97.97623860999-4.157292010633.251149830776.25599135804-1.462388192056.737671830970.03605214533720.3443734883160.150706646011-0.301896550639-0.0943693675045-0.396294691261-0.1405888170710.1654241495260.06714157828970.2050329137040.01906627479250.03078393747060.150194707792-0.01714190829610.141281708562-1.68901574826-7.193681290917.49331772676
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 28 through 51 )28 - 511 - 24
22chain 'A' and (resid 52 through 85 )52 - 8525 - 58
33chain 'A' and (resid 86 through 101 )86 - 10159 - 74
44chain 'A' and (resid 102 through 155 )102 - 15575 - 128
55chain 'A' and (resid 156 through 179 )156 - 179129 - 152
66chain 'A' and (resid 180 through 194 )180 - 194153 - 167
77chain 'A' and (resid 195 through 250 )195 - 250168 - 223
88chain 'A' and (resid 251 through 264 )251 - 264224 - 237
99chain 'A' and (resid 265 through 287 )265 - 287238 - 260

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