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- PDB-3mol: Structure of dimeric holo HasAp H32A Mutant from Pseudomonas aeru... -

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Basic information

Entry
Database: PDB / ID: 3mol
TitleStructure of dimeric holo HasAp H32A Mutant from Pseudomonas aeruginosa to 1.20A Resolution
ComponentsHeme acquisition protein HasAp
KeywordsHEME BINDING PROTEIN / TRANSPORT PROTEIN / hemophore / heme transport / H32A mutation / holo protein
Function / homology
Function and homology information


Heme-binding Protein A; Chain: A; / Haem-binding HasA / Haem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Heme acquisition protein HasAp / Heme acquisition protein HasAp
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsLovell, S. / Battaile, K.P. / Jepkorir, G. / Rodriguez, J.C. / Rui, H. / Im, W. / Alontaga, A.Y. / Yukl, E. / Moenne-Loccoz, P. / Rivera, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Structural, NMR Spectroscopic, and Computational Investigation of Hemin Loading in the Hemophore HasAp from Pseudomonas aeruginosa.
Authors: Jepkorir, G. / Rodriguez, J.C. / Rui, H. / Im, W. / Lovell, S. / Battaile, K.P. / Alontaga, A.Y. / Yukl, E.T. / Rivera, M.
History
DepositionApr 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heme acquisition protein HasAp
B: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9024
Polymers37,6692
Non-polymers1,2332
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-48 kcal/mol
Surface area14170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.740, 52.700, 85.714
Angle α, β, γ (deg.)90.000, 91.480, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11A-317-

HOH

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Components

#1: Protein Heme acquisition protein HasAp


Mass: 18834.467 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-184 / Mutation: H32A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: hasAp, PA14_20020 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD (DE3) / References: UniProt: Q02QP5, UniProt: G3XD33*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.26 M ammonium sulfate, 100 mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 95175 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 19.211 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.96
Reflection shellResolution: 1.2→1.3 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.4 / Num. measured obs: 68621 / Num. unique all: 19526 / Num. unique obs: 19526 / % possible all: 91.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.57 Å19.25 Å
Translation1.57 Å19.25 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MOK
Resolution: 1.2→19.245 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.16 / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.197 4379 5.01 %RANDOM
Rwork0.177 ---
obs0.178 87374 87.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.396 Å2 / ksol: 0.466 e/Å3
Displacement parametersBiso max: 61.66 Å2 / Biso mean: 21.543 Å2 / Biso min: 7.89 Å2
Baniso -1Baniso -2Baniso -3
1--3.825 Å20 Å2-0.275 Å2
2--6.513 Å20 Å2
3----2.688 Å2
Refinement stepCycle: LAST / Resolution: 1.2→19.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 86 305 2979
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.01
X-RAY DIFFRACTIONf_angle_deg1.421
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.2430.2563290.2476879720873
1.243-1.2930.2553600.2217227758776
1.293-1.3520.2334300.2117843827383
1.352-1.4230.234120.1967870828283
1.423-1.5120.2084500.1838301875188
1.512-1.6280.1994410.1728648908991
1.628-1.7920.2124750.1688742921792
1.792-2.0510.1994860.1698929941594
2.051-2.5830.1835000.1679211971197
2.583-19.2470.1784960.179345984197
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)
10.12930.20150.05320.24350.0410.0280.1810.0315-0.08220.0311-0.0640.21530.159-0.07560.00010.1474-0.0136-0.00130.12490.02470.1497-26.5745-6.120436.085
20.21140.06690.09920.034-0.03370.253-0.0849-0.20830.13110.21130.1469-0.08160.0738-0.09510.00410.14870.0205-0.00870.1112-0.02490.1377-20.37630.744741.1079
30.0586-0.1083-0.01640.13670.05980.07350.0101-0.129-0.00390.0878-0.06280.0301-0.049-0.0353-0.00010.13730.0037-0.00340.0938-0.01020.1126-8.9199-1.206243.182
40.1757-0.05480.08590.2831-0.15230.0878-0.15540.1098-0.27320.15370.02550.0390.37330.006-00.19090.0016-0.01230.1167-0.01790.1607-5.7737-10.161242.7808
50.40970.0197-0.28640.40310.12630.2180.0826-0.0505-0.1071-0.0475-0.1249-0.29930.21180.2794-0.00030.15230.01880.00940.1313-0.00730.1474-5.3388-6.464620.2501
60.11310.009-0.11630.18080.16910.21630.04390.0038-0.08960.02170.0203-0.03750.03710.04350.00030.11750.0089-0.01570.071-0.01210.1083-9.4087-4.650729.0984
70.04350.0496-0.09360.0551-0.07470.191-0.13210.1144-0.2393-0.2634-0.0141-0.10740.1458-0.0036-0.00010.13050.0050.02110.15530.02610.1219-6.58533.312814.8159
80.0828-0.0735-0.00310.13880.10610.1242-0.21650.42210.075-0.36220.03050.04990.1220.23150.00040.156-0.0126-0.00550.17230.05570.1398-6.5539.065315.4705
90.0451-0.0144-0.06440.0236-0.03870.1779-0.0170.2705-0.0887-0.12940.0160.15830.2501-0.3041-0.00320.13310.0204-0.00330.09390.00780.1084-17.70541.125817.1067
100.0122-0.0417-0.03980.22180.12090.0849-0.0095-0.08120.01560.09530.0817-0.0591-0.03490.024100.13690.0066-0.01890.0806-0.00750.1349-14.1294-6.723332.112
110.1583-0.01020.08640.1348-0.05290.1049-0.0655-0.0505-0.11960.02890.16-0.18370.26150.20970.01120.1778-0.0027-0.02470.0937-0.0470.1891-10.0534-14.27225.1085
120.0720.062-0.0130.0850.02530.11040.1056-0.1001-0.00680.10950.0677-0.36480.28890.021-0.00030.15990.0022-0.02820.0838-0.0050.1568-17.0905-10.077836.1091
130.3606-0.0459-0.02710.20120.14570.11120.08120.35120.0987-0.16830.05380.10430.0054-0.1578-0.00020.14380.0119-0.00960.15020.03140.1681-24.0301-0.729324.0748
140.05150.033-0.09820.0612-0.05030.14470.0723-0.10430.2740.12960.0225-0.0255-0.2435-0.2039-00.16140.0093-0.01060.13430.03110.1544-14.181611.216915.8606
150.0804-0.0112-0.1070.0486-0.06370.1898-0.00270.11610.20.03510.0051-0.0034-0.19120.09220.00010.14380.0079-0.00350.08230.01890.1312-13.58367.6724.0016
160.4178-0.00840.08310.4031-0.38880.47380.02890.05760.17320.06460.02090.0457-0.0516-0.0214-0.00030.15920.025-0.00110.07780.00290.1486-19.04456.183931.2405
170.049-0.01970.01690.01330.00030.006-0.0882-0.28170.68640.12950.12050.1331-0.4992-0.485-0.00040.16070.0930.01450.29220.01830.2343-35.84246.815231.3648
180.07110.0505-0.00120.07340.0680.08420.08460.02580.1867-0.02570.04560.13-0.067-0.3468-0.00020.16020.03470.01210.16680.01340.1791-29.77753.274338.4472
190.07190.0953-0.05430.1331-0.08610.05110.0496-0.00230.13090.0715-0.09620.2206-0.2713-0.3454-0.00010.1352-0.01510.02470.20710.02310.1904-34.4314-3.083836.8778
200.11170.0542-0.11570.0945-0.03880.10150.5080.1843-0.07480.1367-0.442-0.23520.29510.34760.00090.2065-0.0259-0.03130.17010.03510.1969-25.4342-11.746536.9086
210.05780.0758-0.00860.061-0.01610.0048-0.21840.9475-0.4006-0.1440.1121-0.23170.2594-0.0464-0.00010.1978-0.04130.06130.5193-0.03680.27226.7884-5.195511.4836
220.0090.0223-0.00190.01650.0036-0.00110.09130.808-0.24860.0787-0.494-0.21610.4548-0.02690.00260.202-0.10240.06440.9722-0.00030.213125.49690.47861.3153
230.03890.01760.08250.03230.06270.1333-0.1670.83530.0526-0.0870.0067-0.0761-0.025-0.3963-0.00020.1363-0.07890.01520.74080.13080.16917.0526.16596.3805
240.03120.0376-0.02660.0506-0.00930.0385-0.27190.06990.3398-0.0540.1025-0.09460.2153-0.46130.00060.2024-0.0674-0.00690.73770.09890.188510.61037.0943-2.0203
250.0364-0.01030.0451-0.0014-0.02210.04070.40850.0248-0.06440.2723-0.08540.20720.06870.211-0.00130.3681-0.11810.09390.81890.08130.37593.63230.19980.8334
260.1101-0.0287-0.03110.0926-0.0150.1201-0.35671.064-0.4163-0.1183-0.13180.04570.2908-0.4021-0.00240.1963-0.10150.090.4398-0.15450.23674.4687-6.434819.4651
270.7707-0.42270.44980.7041-0.24080.4765-0.49720.3622-0.47390.08560.03420.14580.1486-0.1409-0.05170.1438-0.05490.05160.1661-0.0730.16855.5569-6.332325.1017
280.0679-0.02390.03190.047-0.11310.1346-0.37690.80260.13060.02410.42210.03130.0811-0.37520.0010.1466-0.09980.01860.50910.01950.14276.3942-0.099613.8297
290.07860.0015-0.05690.0602-0.06390.0593-0.1731.04790.12920.06440.15850.2002-0.2754-0.5424-0.00130.1523-0.05520.01980.67540.04780.18098.05221.29658.6928
300.42330.283-0.25670.2877-0.08640.1284-0.11990.15790.13860.1561-0.0511-0.082-0.15470.0642-0.00910.1409-0.0089-0.01180.10340.01620.11776.53872.12530.1604
310.3937-0.35070.26491.4263-0.73880.5004-0.22730.4247-0.03270.0826-0.0909-0.24470.0280.0325-0.11710.1365-0.03520.03030.19070.02390.161915.6817-2.11325.041
320.10260.09260.03340.09660.03720.0118-0.49261.263-0.1211-0.20450.08680.29060.682-0.39320.00170.2823-0.24710.1180.6645-0.16150.27289.2856-6.439810.2355
330.01050.0065-0.02430.002-0.00840.0313-0.30620.37790.11410.0647-0.26840.15310.50780.05970.00080.2196-0.16360.08770.7303-0.12440.248315.3269-5.58826.007
340.09850.00420.02830.07040.04180.0499-0.38920.266-0.20690.1710.0114-0.00940.54020.16570.00060.1745-0.00730.05320.32710.02910.20622.6395-3.100220.8436
350.0623-0.0052-0.08390.0273-0.0440.1219-0.1360.0620.46640.4311-0.1094-0.3313-0.3210.3878-0.00010.2006-0.0464-0.05160.15680.04350.208913.66575.916332.7274
360.09780.0055-0.07650.0663-0.08450.14920.10750.25890.43010.1785-0.155-0.1224-0.36590.08480.00020.1636-0.02680.00390.20360.08810.208614.19716.980224.3357
370.14640.0526-0.17550.20260.15880.446-0.1250.44290.25590.11230.0871-0.0583-0.1786-0.1319-0.00050.1541-0.01970.01130.37780.11030.200220.52466.302616.7785
380.03990.0255-0.01030.0105-0.01450.0297-0.1411-0.1980.060.3328-0.1389-0.1986-0.19450.05720.00040.1595-0.0383-0.01810.35520.08910.269936.88023.1317.3672
390.0405-0.04830.02450.0957-0.07940.0639-0.20570.95510.11990.11960.0514-0.1858-0.12980.3132-0.00130.1398-0.08640.02560.57650.03120.196730.91323.39097.9932
400.0336-0.0354-0.00570.04170.03240.0359-0.09670.3137-0.398-0.02120.0102-0.2090.47260.27540.00010.1821-0.01210.09950.5558-0.0850.327732.8879-4.76369.4646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 2:12)A2 - 12
2X-RAY DIFFRACTION2(chain A and resid 13:23)A13 - 23
3X-RAY DIFFRACTION3(chain A and resid 24:33)A24 - 33
4X-RAY DIFFRACTION4(chain A and resid 34:41)A34 - 41
5X-RAY DIFFRACTION5(chain A and resid 42:52)A42 - 52
6X-RAY DIFFRACTION6(chain A and resid 53:71)A53 - 71
7X-RAY DIFFRACTION7(chain A and resid 72:79)A72 - 79
8X-RAY DIFFRACTION8(chain A and resid 80:85)A80 - 85
9X-RAY DIFFRACTION9(chain A and resid 86:90)A86 - 90
10X-RAY DIFFRACTION10(chain A and resid 91:98)A91 - 98
11X-RAY DIFFRACTION11(chain A and resid 99:109)A99 - 109
12X-RAY DIFFRACTION12(chain A and resid 110:114)A110 - 114
13X-RAY DIFFRACTION13(chain A and resid 115:122)A115 - 122
14X-RAY DIFFRACTION14(chain A and resid 123:130)A123 - 130
15X-RAY DIFFRACTION15(chain A and resid 131:138)A131 - 138
16X-RAY DIFFRACTION16(chain A and resid 139:156)A139 - 156
17X-RAY DIFFRACTION17(chain A and resid 157:162)A157 - 162
18X-RAY DIFFRACTION18(chain A and resid 163:169)A163 - 169
19X-RAY DIFFRACTION19(chain A and resid 170:177)A170 - 177
20X-RAY DIFFRACTION20(chain A and resid 178:184)A178 - 184
21X-RAY DIFFRACTION21(chain B and resid 2:8)B2 - 8
22X-RAY DIFFRACTION22(chain B and resid 9:15)B9 - 15
23X-RAY DIFFRACTION23(chain B and resid 16:28)B16 - 28
24X-RAY DIFFRACTION24(chain B and resid 29:35)B29 - 35
25X-RAY DIFFRACTION25(chain B and resid 36:42)B36 - 42
26X-RAY DIFFRACTION26(chain B and resid 43:48)B43 - 48
27X-RAY DIFFRACTION27(chain B and resid 49:55)B49 - 55
28X-RAY DIFFRACTION28(chain B and resid 56:60)B56 - 60
29X-RAY DIFFRACTION29(chain B and resid 61:68)B61 - 68
30X-RAY DIFFRACTION30(chain B and resid 69:84)B69 - 84
31X-RAY DIFFRACTION31(chain B and resid 85:92)B85 - 92
32X-RAY DIFFRACTION32(chain B and resid 93:108)B93 - 108
33X-RAY DIFFRACTION33(chain B and resid 109:114)B109 - 114
34X-RAY DIFFRACTION34(chain B and resid 115:122)B115 - 122
35X-RAY DIFFRACTION35(chain B and resid 123:129)B123 - 129
36X-RAY DIFFRACTION36(chain B and resid 130:138)B130 - 138
37X-RAY DIFFRACTION37(chain B and resid 139:156)B139 - 156
38X-RAY DIFFRACTION38(chain B and resid 157:163)B157 - 163
39X-RAY DIFFRACTION39(chain B and resid 164:170)B164 - 170
40X-RAY DIFFRACTION40(chain B and resid 171:180)B171 - 180

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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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