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- PDB-7szp: Crystal Structure of Histidinol-phosphate aminotransferase from K... -

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Basic information

Entry
Database: PDB / ID: 7szp
TitleCrystal Structure of Histidinol-phosphate aminotransferase from Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)
ComponentsHistidinol-phosphate aminotransferase
KeywordsTRANSFERASE / SSGCID / Histidinol-phosphate aminotransferase / hisC / L-histidine biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


histidinol-phosphate transaminase / histidinol-phosphate transaminase activity / L-histidine biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Histidinol-phosphate aminotransferase family / Aminotransferase, class-II, pyridoxal-phosphate binding site / Aminotransferases class-II pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
ACETATE ION / PYRIDOXAL-5'-PHOSPHATE / Histidinol-phosphate aminotransferase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: to be published
Title: Crystal Structure of Histidinol-phosphate aminotransferase from Klebsiella pneumoniae subsp. pneumoniae (strain HS11286)
Authors: Abendroth, J. / DeBouver, N.D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidinol-phosphate aminotransferase
B: Histidinol-phosphate aminotransferase
C: Histidinol-phosphate aminotransferase
D: Histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,34328
Polymers159,1864
Non-polymers2,15724
Water27,3291517
1
A: Histidinol-phosphate aminotransferase
B: Histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,66914
Polymers79,5932
Non-polymers1,07612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9520 Å2
ΔGint-24 kcal/mol
Surface area24610 Å2
MethodPISA
2
C: Histidinol-phosphate aminotransferase
D: Histidinol-phosphate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,67414
Polymers79,5932
Non-polymers1,08112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10180 Å2
ΔGint-26 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.400, 111.610, 119.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Histidinol-phosphate aminotransferase / Imidazole acetol-phosphate transaminase


Mass: 39796.461 Da / Num. of mol.: 4 / Fragment: KlpnC.00674.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: hisC, BANRA_00698, BN49_3694, C3F39_24445, DBX64_10115, DD583_14750, DRB11_00465, GJJ08_009030, GTH21_13695, NCTC11679_01843, NCTC13465_03304, NCTC204_04368, NCTC3279_02744, NCTC5052_02322, ...Gene: hisC, BANRA_00698, BN49_3694, C3F39_24445, DBX64_10115, DD583_14750, DRB11_00465, GJJ08_009030, GTH21_13695, NCTC11679_01843, NCTC13465_03304, NCTC204_04368, NCTC3279_02744, NCTC5052_02322, NCTC5053_06444, NCTC8849_04067, NCTC9128_08148, NCTC9645_00032, NCTC9661_02650, SAMEA3499901_05026, SAMEA3515130_03500, SAMEA3538828_00142, SAMEA3649466_00212, SAMEA3729663_00211, SAMEA4364603_01150
Plasmid: KlpnC.00674.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: W9BAC7, histidinol-phosphate transaminase

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Non-polymers , 6 types, 1541 molecules

#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1517 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.34 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Anatract/Microlytic MCSG1 screen, condition B6: 200mM Calcium acetate, 100mM MES / NaOH pH 6.0: 25% (w/V) PEG 8000: KlpnC.00674.a.B1.PW39002 at 33.5mg/ml: over night soak with 2.5mM PLP in ...Details: Anatract/Microlytic MCSG1 screen, condition B6: 200mM Calcium acetate, 100mM MES / NaOH pH 6.0: 25% (w/V) PEG 8000: KlpnC.00674.a.B1.PW39002 at 33.5mg/ml: over night soak with 2.5mM PLP in DMSO: tra: 322257 b6: cryo: 20% EG + soak: puck: jql0-1.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 4, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 129492 / % possible obs: 98.3 % / Redundancy: 6.178 % / Biso Wilson estimate: 27.82 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.055 / Χ2: 0.953 / Net I/σ(I): 23.28
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.855.6870.423.6491220.90.46394.7
1.85-1.96.2570.333592060.950.36397.7
1.9-1.956.2630.2676.4889560.9670.29197.9
1.95-2.016.3010.2048.3586810.980.22297.9
2.01-2.086.2270.16210.5684830.9860.17798.1
2.08-2.156.2780.12913.0982000.9910.1498.4
2.15-2.236.2630.10815.4279550.9930.11898.4
2.23-2.326.1820.0918.4276270.9950.09998.2
2.32-2.436.2540.07820.9773620.9960.08598.6
2.43-2.556.2630.06823.5970340.9970.07598.6
2.55-2.686.240.05628.1967120.9980.06298.7
2.68-2.856.2440.04931.5763760.9980.05398.9
2.85-3.046.2360.0437.3460120.9990.04499
3.04-3.296.2080.03642.0856260.9990.03999.4
3.29-3.66.1640.03147.4952010.9990.03499.4
3.6-4.026.1190.02752.1947140.9990.0399.5
4.02-4.656.1280.02555.642230.9990.02799.8
4.65-5.696.0750.02555.2335860.9990.02799.7
5.69-8.055.9690.02554.728120.9990.02799.8
8.05-505.5460.02358.0616040.9990.02597.6

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Processing

Software
NameVersionClassification
PHENIX1.20rc3-4406refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1fg7A as per Morda

Resolution: 1.8→44.55 Å / SU ML: 0.1761 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.5298
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2035 1.57 %0
Rwork0.1512 127427 --
obs0.1519 129462 98.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.62 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10704 0 138 1517 12359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007911192
X-RAY DIFFRACTIONf_angle_d0.910115296
X-RAY DIFFRACTIONf_chiral_restr0.05921785
X-RAY DIFFRACTIONf_plane_restr0.00982046
X-RAY DIFFRACTIONf_dihedral_angle_d12.75964167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.25431160.20468073X-RAY DIFFRACTION94.39
1.84-1.890.22741360.18018350X-RAY DIFFRACTION97.67
1.89-1.940.24671420.17578338X-RAY DIFFRACTION97.73
1.94-20.21111420.17588415X-RAY DIFFRACTION97.88
2-2.060.18711190.15728418X-RAY DIFFRACTION98.23
2.06-2.130.2291390.16028423X-RAY DIFFRACTION98.06
2.13-2.220.21961560.15598416X-RAY DIFFRACTION98.31
2.22-2.320.23421100.15778464X-RAY DIFFRACTION98.29
2.32-2.440.20531460.15448487X-RAY DIFFRACTION98.73
2.44-2.60.211240.15718516X-RAY DIFFRACTION98.35
2.6-2.80.20521260.15598552X-RAY DIFFRACTION98.79
2.8-3.080.19931480.1548577X-RAY DIFFRACTION99.18
3.08-3.520.19921450.14658637X-RAY DIFFRACTION99.34
3.52-4.440.15071690.12548734X-RAY DIFFRACTION99.56
4.44-44.550.16031170.14519027X-RAY DIFFRACTION99.47
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)
11.720793375660.0440384614129-0.903424317341.68530897897-0.3456314842361.979843142270.1345179772460.1767110549740.0765038603789-0.177943075764-0.0688870332956-0.229343355217-0.0377396336285-0.0644287603167-0.06079737480420.1308977563490.02204803452120.04582463168330.1749819074390.01415806054530.14328156328981.309603990411.3194596386-28.6160107457
21.55732107407-0.717790265588-1.232617990591.061188913760.3915070829072.151427922590.3689263601490.2101246109390.426967099335-0.247479689739-0.00735979162972-0.215131601424-0.48188890827-0.149353996941-0.2246139851020.2395641845010.05285925434780.1147982701570.1785238038320.05505243424910.23614951776972.013684848824.7008445556-22.5762744221
36.68834214660.02503372748880.5939396931885.94747768546-0.5728298976488.65265900573-0.181402702056-0.3773117224140.4173456075850.440297348245-0.0116655987061-0.284108629127-0.6392128724370.01304117301450.2344492326940.1904753752780.00166109751397-0.007608513289180.171685249052-0.009477760595050.201849945037-8.1434931790919.2911887808-27.1385610491
42.458995386960.685340540945-0.5339799960945.863187564151.41125892772.154866861610.03935730051660.1801780936340.41275685657-0.259345977692-0.07382339762130.250017816202-0.4650057621810.009816318174820.08203155010360.225633458673-0.009075262951560.002138454231080.1610808641120.02615529742450.2016570535343.1701629634119.46591472431.52195239645
50.744959849887-0.0216301426436-1.293166865040.02713213623390.06399244196152.20348889374-0.0198056406003-0.1186542602990.07716439478530.01172365823150.0652151960782-0.092191367822-0.09839854343120.334588954806-0.07205889634390.1472147270240.01014159154820.003080951922930.232005676664-0.004110154903010.23828017472723.41977138099.93552442895-13.2177814475
62.642061216760.4758795523580.04204732648552.33213492647-0.3832279893192.89975549933-0.0262494004339-0.122145605732-0.2228830314530.08152725834430.00141224095416-0.3445225889570.3906182292190.2925865950410.01513693733440.1575837554930.05337985089390.002936488981060.147309365936-0.008817935014750.19445599225515.1464829343-4.64229164723-10.6696574477
71.212446415250.0885962251399-0.2364357955250.891076988644-0.09237874354031.69613748728-0.0452376474580.059218430127-0.0647896574379-0.03062791465110.01771131950130.04909221969080.128568753082-0.1277444684320.02302893893530.133248480395-0.008454463631540.02268794260.0942374424737-0.001759796826040.159039913971-8.4909105984-2.43945031194-12.9823109176
80.6110596555830.221428096344-0.06647253452190.9131653357650.396663645621.39343433049-0.0288029093361-0.0405805946288-0.08026677069390.01052257875820.00445127765193-0.03784628858480.1698879122260.06508897202550.02283129482810.1257643523690.02679166669610.008400229350870.109058737140.009220521198690.1653017025137.63888825501-2.15960527731-10.6570000106
92.10645240291-0.225207191501-0.07244710378212.037299394910.5911185797351.59056307974-0.049092036845-0.3160111614710.05976081975480.3378201853-0.0859086349690.27574734790.0995876870905-0.1143613951890.1238570168110.179974593013-0.02263314521330.04194203945310.160996848325-0.01012962654010.158327625107-3.081539885328.802903990819.3096098892
101.964763184830.54539358420.8076974607211.941255126130.4197879292121.8985465770.00706705214723-0.0962448516120.2382203015720.205024813996-0.1801341517730.401115544662-0.0591366004368-0.1648454623520.1632913579990.1867360933920.01150272523150.0560143019370.166842222754-0.0465945558650.249378249643-7.4459158135115.63206324777.36432574621
110.00927126162973-0.04505133907250.03982963578730.402547579494-0.3307594971780.159194337214-0.08853022834330.0848291239415-0.249258324871-0.05391579008720.0800529148831-0.1507462355070.1860180328420.1389647102270.01013310379610.262943479674-0.01066129222070.04153500169620.244974502191-0.03787936146380.24647388680510.8175393293-3.05758225226-29.3669700524
120.4641667316620.000771322990358-0.05586353108470.298204049392-0.09620940458061.238800219170.01322231545740.02811877744190.0025966642655-0.04706777038260.0277973003875-0.0804579782584-0.0240997825310.197910642831-0.04305135347870.122031988364-0.01690607538160.02387434472450.113403496783-0.01672196219890.1602363516317.383588229518.4086021395-32.7001493812
131.076338042930.106428414681-0.2698661673460.573584602458-0.6251852893550.512669636094-0.0412317605880.31649994394-0.160145144961-0.2083609367830.09261569943250.08730731236470.17362362869-0.305337337423-0.02850152605290.215071863825-0.0768393885959-0.005488156822610.274019941006-0.0284391791260.17006524254657.10154354794.63962658781-17.6619202191
141.26304865250.421058466049-0.6154447514961.20680475975-0.5664500899981.30748379488-0.1248265879780.0201355653364-0.151253862389-0.1284951748310.0450069288858-0.09757349856910.239338284515-0.05150834244950.07706367278870.158858985557-0.05138781293860.01032741444210.151435369876-0.02730856733550.13277456772764.2434874986-9.71729293525-3.68245908408
150.8660519618760.0783078452816-0.5540309492281.5584541254-1.131307313391.60920710072-0.1144979525990.1430412918050.00189866352474-0.3237764477310.3073359021060.3412542902860.410359362642-0.580373398973-0.04463245504230.214564048689-0.187871884956-0.06303673782930.352113347730.009996120687850.1635316499347.9476755348-6.38955330752-7.96917342776
160.432603165458-1.200131271840.07866750880943.02250457919-0.3044810040830.0116228629148-0.20973163358-0.2332933633710.0392402852770.5874290573970.291833839886-0.00537192820108-0.09752769668130.000548966026167-0.08587289348450.2450379914150.0153778593310.05350094298580.2316969346170.003377683061180.24160086516276.89136724410.792226773-5.83579292667
170.4828915617440.0217464807512-0.5456758895470.60396554623-0.3945442039390.790586763440.1175150252640.4506919084770.114563250219-0.06109829576070.05097220164050.159205807073-0.0237526401513-0.444968142603-0.1667254026530.151381572220.03233423451450.004925826614390.4158536481060.05149487757010.19491418441655.145757373914.9530560166-22.9693740287
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 80 through 171 )DV80 - 17180 - 171
22chain 'D' and (resid 172 through 351 )DV172 - 351172 - 351
33chain 'A' and (resid 0 through 18 )AA0 - 181 - 19
44chain 'A' and (resid 19 through 38 )AA19 - 3820 - 39
55chain 'A' and (resid 39 through 57 )AA39 - 5740 - 58
66chain 'A' and (resid 58 through 79 )AA58 - 7959 - 80
77chain 'A' and (resid 80 through 172 )AA80 - 17281 - 173
88chain 'A' and (resid 173 through 255 )AA173 - 255174 - 256
99chain 'A' and (resid 256 through 313 )AA256 - 313257 - 314
1010chain 'A' and (resid 314 through 352 )AA314 - 352315 - 353
1111chain 'B' and (resid -2 through 34 )BH-2 - 341 - 31
1212chain 'B' and (resid 35 through 353 )BH35 - 35332 - 350
1313chain 'C' and (resid 1 through 57 )CO1 - 571 - 52
1414chain 'C' and (resid 58 through 199 )CO58 - 19953 - 194
1515chain 'C' and (resid 200 through 352 )CO200 - 352195 - 347
1616chain 'D' and (resid 1 through 33 )DV1 - 331 - 33
1717chain 'D' and (resid 34 through 79 )DV34 - 7934 - 79

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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