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- PDB-9nh3: Helicobacter pylori strain SS1 KatA -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9nh3
TitleHelicobacter pylori strain SS1 KatA
ComponentsCatalase
KeywordsOXIDOREDUCTASE / catalase / oxidative stress
Function / homology
Function and homology information


catalase / catalase activity / hydrogen peroxide catabolic process / response to hydrogen peroxide / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain ...Catalase, clade 3 / Catalase, mono-functional, haem-containing, clades 1 and 3 / Catalase haem-binding site / Catalase proximal heme-ligand signature. / Catalase / Catalase immune-responsive domain / Catalase-related immune-responsive / Catalase active site / Catalase proximal active site signature. / Catalase core domain / Catalase, mono-functional, haem-containing / Catalase / catalase family profile. / Catalase superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Catalase
Similarity search - Component
Biological speciesHelicobacter pylori SS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsBaylink, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)4R00AI148587-03 United States
CitationJournal: Biorxiv / Year: 2025
Title: AlphaFold 3 accurately models natural variants of Helicobacter pylori catalase KatA.
Authors: Baylink, A.
History
DepositionFeb 23, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 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: Catalase
B: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,06913
Polymers117,4782
Non-polymers1,59111
Water21,4561191
1
A: Catalase
B: Catalase
hetero molecules

A: Catalase
B: Catalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,13726
Polymers234,9564
Non-polymers3,18122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area50190 Å2
ΔGint-384 kcal/mol
Surface area58140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.512, 96.198, 154.754
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-715-

HOH

21B-823-

HOH

31B-1168-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Catalase


Mass: 58739.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori SS1 (bacteria) / Gene: katA / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: F4ZZ52, catalase

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Non-polymers , 5 types, 1202 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1191 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.14 Å3/Da / Density % sol: 42.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M sodium acetate, pH 4.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→55.3 Å / Num. obs: 84023 / % possible obs: 100 % / Redundancy: 12.94 % / Biso Wilson estimate: 15.86 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.45
Reflection shellResolution: 1.87→1.94 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 8292 / CC1/2: 0.57 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootmodel building
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→55.3 Å / SU ML: 0.1868 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.2918
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.191 2000 2.38 %
Rwork0.1418 82015 -
obs0.143 84015 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.26 Å2
Refinement stepCycle: LAST / Resolution: 1.87→55.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8013 0 105 1191 9309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01038491
X-RAY DIFFRACTIONf_angle_d0.998711533
X-RAY DIFFRACTIONf_chiral_restr0.05821134
X-RAY DIFFRACTIONf_plane_restr0.01171506
X-RAY DIFFRACTIONf_dihedral_angle_d15.43613133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.920.29831400.24295767X-RAY DIFFRACTION99.95
1.92-1.970.23991410.20975767X-RAY DIFFRACTION100
1.97-2.030.24671420.19055818X-RAY DIFFRACTION100
2.03-2.090.24741410.18465788X-RAY DIFFRACTION100
2.09-2.170.20911410.17145796X-RAY DIFFRACTION100
2.17-2.250.22531420.15725822X-RAY DIFFRACTION100
2.25-2.360.20441420.14175790X-RAY DIFFRACTION100
2.36-2.480.20771420.13365823X-RAY DIFFRACTION100
2.48-2.640.1761420.12675850X-RAY DIFFRACTION100
2.64-2.840.16131430.13025845X-RAY DIFFRACTION100
2.84-3.120.19061440.12545883X-RAY DIFFRACTION99.98
3.12-3.580.17371430.12025913X-RAY DIFFRACTION100
3.58-4.510.14241460.10585952X-RAY DIFFRACTION100
4.51-55.30.17231510.13826201X-RAY DIFFRACTION99.92
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)
10.349159921964-0.502987286496-0.1819063157223.460275319290.4359020834390.1034742587580.04571540178830.134122647907-0.0975150421763-0.261085208776-0.06722216322680.2696482860610.065776988961-0.01707231515780.01875347321540.167517213746-0.0208332125512-0.03509037681540.148146623993-0.03447090290770.12237582800418.8032794575-37.3888268226-32.8369171221
23.44909789576-0.634863794095-0.5151916305963.063677063871.303089335312.35247011588-0.107065773725-0.058341038087-0.4040161986650.162642103455-0.04831515990250.2614070142150.457776064921-0.2089680751560.1508934805770.246893156471-0.0629962104030.00458515537930.106162416431-0.0216792657620.22008418248416.6328203674-56.2262289487-17.6547715272
30.211235738569-0.04994051089790.3287797511730.388309139325-0.2007430354571.698442417060.00698052720074-0.04001947391550.03167688124120.09938657277110.01270078984730.0575762880794-0.00833479188818-0.0850080327087-0.02155006177670.0805632063055-0.007477885328270.01943966568160.0730459446375-0.0043642142630.090150065932831.1019739706-9.9896703272719.4210383668
42.991298424930.5308790880280.823787162171.039990970270.9422102402221.85794266059-0.0537936939398-0.05212042831640.0675839767891-0.0590247556513-0.07782051512760.25477883526-0.0437824228295-0.3287347822550.1245970438860.07109691009110.00630065192514-0.008892451948150.1398730974190.02052438535970.1551991861184.09410930504-1.58208539207-12.3883194258
50.9854962640690.178732217878-0.2054871009390.393652591673-0.05525208962080.5613982885290.006186008931240.02579276632920.108564650165-0.0413589914502-0.002501933187390.0141732229238-0.0623863066341-0.00767930842638-0.004750493380450.1058807292550.00714346108739-0.005635277155830.09623346201530.01258683250030.10588710094927.48557094185.23623902859-14.9654230888
60.6643892467260.3264176602190.2731472375222.466500845971.112433700191.648859268190.02715400796030.05461392624540.116222141413-0.139671709023-0.1003212909250.186198105407-0.0814109872534-0.2480790715630.07479667071750.07034232999090.0248222199513-0.01721722787770.1456005678320.02449483807040.12166563549511.08974377523.23612473675-20.6905351526
71.016670797020.101066660573-0.01090742536230.6521055942320.5440353187822.40500449898-0.03836427472430.06021455815830.132964377631-0.102709365095-0.01512330800910.121821466784-0.140648654189-0.2085081842470.06280988554980.09327487563710.027227091863-0.02251425331530.04297569544840.03781923810930.14022860384814.19861521758.16614973894-16.4225192874
80.3359578202730.0416203938638-0.01831448811950.544993785184-0.128261714710.51369745849-0.00126023583720.04706441971370.0130869038817-0.085853302910.01732533254430.07870300228770.0584586570199-0.069676091407-0.01817785448950.0879635568775-0.00127948798999-0.011448724510.121925336909-0.0004831512297340.12012415782118.4123765413-11.7740403281-16.8003143649
93.31828508855-1.4238006372-0.1373108253393.02389557597-0.5095501833492.36083183032-0.05317345278050.084124228080.4993292708-0.04206032179050.052204022301-0.168690780057-0.3111920804910.1660256089770.01021547618010.17729264875-0.03818034943680.00444053244920.09805253247370.04904040979340.20833860233236.63606036921.4371595813-24.6441355307
100.7523881526480.1997626628310.7791854761820.5050330521710.1626434042581.601147511490.0209305781056-0.0151983047617-0.0990172354140.06543688564150.0172190539817-0.1486574238010.1208835069880.110360645593-0.02143154219650.07527276596960.0191385851912-0.002267290186720.06908764315180.007715550088420.10809443599248.4058256313-25.097034397213.5697230238
111.02069796956-0.152852962799-0.1587527608910.858020528135-0.3410286591521.4288162324-0.0005197290245470.124408364969-0.0567315399265-0.164707132523-0.0388577147521-0.1348118014530.1004242823030.1768374815770.03990620893850.1533953764270.03032430445030.02665506790250.109759553172-0.03251492487130.11485371937649.9306044802-33.1560687022-27.7764817205
123.317440879842.37010171526-2.114463135522.05660068032-2.129455032332.39619487710.111262867239-0.005496536653970.0521826736940.1070858218610.03859245270730.05037511475630.0611759767158-0.0285791345873-0.1454437366730.1520280351880.0318515647607-0.01787902905110.0669261472484-0.02032646630750.10311353203337.7787445925-38.8228978627-12.3124377735
130.6951117075790.147100860472-0.1015710419310.4885173389670.06589670998530.54678695952-0.03518343499250.0637403311833-0.120136591339-0.05257956223740.01201360159010.03485377587180.160096675158-0.031257709550.0203391961420.145267835408-0.00495694296227-0.01400244437380.0822653708234-0.01903617656490.10243877268226.8528901378-40.3888793688-16.8020829887
140.602245540678-0.09065285686160.08019632060842.21936152734-1.153759922151.20389959237-0.003407379985610.141901784836-0.098060488156-0.413659069811-0.0190968271806-0.08738579440120.3385411696890.04175890214140.03640719572470.2016149053910.0135832561952-0.0002347829862090.121208708318-0.04583563238930.10441929885139.2962674321-37.9153971664-30.2292054479
151.27730341896-0.1023613577550.3549661309560.563285977502-0.1734783898821.33021792470.006530181671250.120435703597-0.0978822791452-0.0979421883952-0.0132719785161-0.0339954623780.2139626649880.06931465501660.003652517930170.1883746904120.01742810543180.001704118944290.0534059764242-0.04820784880450.11605884319439.5144661209-42.9135888252-24.4802812919
160.3056225185950.08414316537940.2203520459820.3357343753410.003405984899661.113407069210.02708103788050.0684131846904-0.0279849858016-0.0523762893306-0.0156548492464-0.02881074333720.03045012803850.0805395973706-0.007448650841040.1187120095710.01416583378770.02121949506650.0966485935262-0.00814280077290.10280381476540.1086371283-25.09180967-16.2698337566
171.382742951780.491776530031.201323345090.7592772422890.5857394324191.48190442972-0.02051147312930.2028151464470.076011158475-0.1396653949490.0370922704161-0.04786698702120.04914502332050.186600821061-0.01711936775010.1150399842870.01393616945230.03734986463460.1118753962320.01465622506160.10622851655442.8565106649-9.2527767509-23.530906553
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 407 through 437 )BC407 - 437406 - 436
22chain 'B' and (resid 438 through 491 )BC438 - 491437 - 490
33chain 'A' and (resid 4 through 58 )AA4 - 581 - 55
44chain 'A' and (resid 59 through 95 )AA59 - 9556 - 92
55chain 'A' and (resid 96 through 192 )AA96 - 19293 - 189
66chain 'A' and (resid 193 through 227 )AA193 - 227190 - 224
77chain 'A' and (resid 228 through 302 )AA228 - 302225 - 299
88chain 'A' and (resid 303 through 437 )AA303 - 437300 - 434
99chain 'A' and (resid 438 through 491 )AA438 - 491435 - 488
1010chain 'B' and (resid 2 through 58 )BC2 - 581 - 57
1111chain 'B' and (resid 59 through 95 )BC59 - 9558 - 94
1212chain 'B' and (resid 96 through 119 )BC96 - 11995 - 118
1313chain 'B' and (resid 120 through 192 )BC120 - 192119 - 191
1414chain 'B' and (resid 193 through 227 )BC193 - 227192 - 226
1515chain 'B' and (resid 228 through 302 )BC228 - 302227 - 301
1616chain 'B' and (resid 303 through 362 )BC303 - 362302 - 361
1717chain 'B' and (resid 363 through 406 )BC363 - 406362 - 405

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