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- PDB-7o49: Crystal structure of Penicillin-Binding Protein 1 (PBP1) from Sta... -

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Basic information

Entry
Database: PDB / ID: 7o49
TitleCrystal structure of Penicillin-Binding Protein 1 (PBP1) from Staphylococcus aureus
ComponentsPenicillin-binding protein 1
KeywordsHYDROLASE / Cell division / antibiotic resistance / peptidoglycan synthesis / transpeptidase
Function / homology
Function and homology information


penicillin binding / integral component of membrane
Similarity search - Function
PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
: / Penicillin-binding protein 1
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus COL (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsMartinez Caballero, S. / Hermoso, J.A.
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: Integrative structural biology of the penicillin-binding protein-1 from Staphylococcus aureus , an essential component of the divisome machinery.
Authors: Martinez-Caballero, S. / Mahasenan, K.V. / Kim, C. / Molina, R. / Feltzer, R. / Lee, M. / Bouley, R. / Hesek, D. / Fisher, J.F. / Munoz, I.G. / Chang, M. / Mobashery, S. / Hermoso, J.A.
History
DepositionApr 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 1
B: Penicillin-binding protein 1
C: Penicillin-binding protein 1
D: Penicillin-binding protein 1
E: Penicillin-binding protein 1
F: Penicillin-binding protein 1
G: Penicillin-binding protein 1
H: Penicillin-binding protein 1
I: Penicillin-binding protein 1
J: Penicillin-binding protein 1
K: Penicillin-binding protein 1
L: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)872,08740
Polymers868,29612
Non-polymers3,79128
Water90150
1
A: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7093
Polymers72,3581
Non-polymers3512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7093
Polymers72,3581
Non-polymers3512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7444
Polymers72,3581
Non-polymers3863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7444
Polymers72,3581
Non-polymers3863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7444
Polymers72,3581
Non-polymers3863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7444
Polymers72,3581
Non-polymers3863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7093
Polymers72,3581
Non-polymers3512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7444
Polymers72,3581
Non-polymers3863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7093
Polymers72,3581
Non-polymers3512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7444
Polymers72,3581
Non-polymers3863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3932
Polymers72,3581
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: Penicillin-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3932
Polymers72,3581
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)311.862, 197.148, 221.596
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18A
28I
19A
29J
110A
210K
111A
211L
112B
212C
113B
213D
114B
214E
115B
215F
116B
216G
117B
217H
118B
218I
119B
219J
120B
220K
121B
221L
122C
222D
123C
223E
124C
224F
125C
225G
126C
226H
127C
227I
128C
228J
129C
229K
130C
230L
131D
231E
132D
232F
133D
233G
134D
234H
135D
235I
136D
236J
137D
237K
138D
238L
139E
239F
140E
240G
141E
241H
142E
242I
143E
243J
144E
244K
145E
245L
146F
246G
147F
247H
148F
248I
149F
249J
150F
250K
151F
251L
152G
252H
153G
253I
154G
254J
155G
255K
156G
256L
157H
257I
158H
258J
159H
259K
160H
260L
161I
261J
162I
262K
163I
263L
164J
264K
165J
265L
166K
266L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A64 - 590
2010B64 - 590
1020A64 - 588
2020C64 - 588
1030A64 - 588
2030D64 - 588
1040A64 - 590
2040E64 - 590
1050A64 - 591
2050F64 - 591
1060A64 - 588
2060G64 - 588
1070A109 - 589
2070H64 - 589
1080A64 - 588
2080I64 - 588
1090A64 - 590
2090J64 - 590
10100A64 - 589
20100K64 - 589
10110A64 - 587
20110L64 - 587
10120B64 - 589
20120C64 - 589
10130B64 - 589
20130D64 - 589
10140B64 - 590
20140E64 - 590
10150B64 - 589
20150F64 - 589
10160B64 - 589
20160G64 - 589
10170B109 - 589
20170H64 - 589
10180B64 - 589
20180I64 - 589
10190B64 - 590
20190J64 - 590
10200B64 - 589
20200K64 - 589
10210B64 - 586
20210L64 - 586
10220C64 - 588
20220D64 - 588
10230C64 - 589
20230E64 - 589
10240C64 - 589
20240F64 - 589
10250C64 - 589
20250G64 - 589
10260C109 - 588
20260H64 - 588
10270C64 - 589
20270I64 - 589
10280C64 - 589
20280J64 - 589
10290C64 - 589
20290K64 - 589
10300C64 - 587
20300L64 - 587
10310D64 - 588
20310E64 - 588
10320D64 - 589
20320F64 - 589
10330D64 - 588
20330G64 - 588
10340D64 - 588
20340H64 - 588
10350D64 - 588
20350I64 - 588
10360D64 - 588
20360J64 - 588
10370D64 - 589
20370K64 - 589
10380D64 - 587
20380L64 - 587
10390E64 - 590
20390F64 - 590
10400E64 - 589
20400G64 - 589
10410E109 - 589
20410H64 - 589
10420E64 - 589
20420I64 - 589
10430E64 - 590
20430J64 - 590
10440E64 - 589
20440K64 - 589
10450E64 - 587
20450L64 - 587
10460F64 - 589
20460G64 - 589
10470F109 - 589
20470H64 - 589
10480F64 - 589
20480I64 - 589
10490F64 - 590
20490J64 - 590
10500F64 - 589
20500K64 - 589
10510F64 - 586
20510L64 - 586
10520G109 - 588
20520H64 - 588
10530G64 - 589
20530I64 - 589
10540G64 - 589
20540J64 - 589
10550G64 - 589
20550K64 - 589
10560G64 - 587
20560L64 - 587
10570H64 - 588
20570I109 - 588
10580H64 - 589
20580J109 - 589
10590H64 - 588
20590K64 - 588
10600H64 - 586
20600L64 - 586
10610I64 - 589
20610J64 - 589
10620I64 - 589
20620K64 - 589
10630I64 - 587
20630L64 - 587
10640J64 - 589
20640K64 - 589
10650J64 - 587
20650L64 - 587
10660K64 - 587
20660L64 - 587

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66

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Components

#1: Protein
Penicillin-binding protein 1


Mass: 72358.016 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus COL (bacteria)
Gene: pbp1, SACOL1194 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2WVW5
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.92 Å3/Da / Density % sol: 68.64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: D,L-malic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3.03→49.015 Å / Num. obs: 145321 / % possible obs: 89.8 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.058 / Net I/σ(I): 11
Reflection shellResolution: 3.033→3.416 Å / Rmerge(I) obs: 1.195 / Num. unique obs: 7266 / Rpim(I) all: 0.401

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TRO
Resolution: 3.03→49 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.869 / SU B: 20.443 / SU ML: 0.341 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.549 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 7237 5 %RANDOM
Rwork0.2111 ---
obs0.2128 138083 55.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 328.92 Å2 / Biso mean: 93.555 Å2 / Biso min: 17.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å20 Å2
2--1.27 Å2-0 Å2
3----1.25 Å2
Refinement stepCycle: final / Resolution: 3.03→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms48489 0 167 50 48706
Biso mean--134.53 45.62 -
Num. residues----6154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01349701
X-RAY DIFFRACTIONr_bond_other_d0.0020.01747437
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.6566852
X-RAY DIFFRACTIONr_angle_other_deg1.2131.591109817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.11556127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67623.6852461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.215159063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.63815210
X-RAY DIFFRACTIONr_chiral_restr0.0650.26161
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0256210
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0211258
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A164390.1
12B164390.1
21A165720.09
22C165720.09
31A157430.1
32D157430.1
41A165680.09
42E165680.09
51A164860.1
52F164860.1
61A165690.09
62G165690.09
71A144570.1
72H144570.1
81A164690.09
82I164690.09
91A165120.1
92J165120.1
101A159230.1
102K159230.1
111A153760.11
112L153760.11
121B164230.1
122C164230.1
131B159910.1
132D159910.1
141B167110.1
142E167110.1
151B167900.1
152F167900.1
161B165640.1
162G165640.1
171B143190.11
172H143190.11
181B165590.09
182I165590.09
191B165080.1
192J165080.1
201B161320.1
202K161320.1
211B154670.11
212L154670.11
221C158510.1
222D158510.1
231C164850.1
232E164850.1
241C164620.1
242F164620.1
251C167980.08
252G167980.08
261C145610.1
262H145610.1
271C166270.08
272I166270.08
281C167260.09
282J167260.09
291C160520.1
292K160520.1
301C155000.1
302L155000.1
311D159630.09
312E159630.09
321D159940.11
322F159940.11
331D157640.1
332G157640.1
341D151210.09
342H151210.09
351D157090.09
352I157090.09
361D158340.09
362J158340.09
371D161430.1
372K161430.1
381D155560.11
382L155560.11
391E167640.09
392F167640.09
401E166090.09
402G166090.09
411E143810.1
412H143810.1
421E164970.09
422I164970.09
431E165080.1
432J165080.1
441E162410.09
442K162410.09
451E155550.1
452L155550.1
461F165560.09
462G165560.09
471F143180.11
472H143180.11
481F164130.09
482I164130.09
491F164980.1
492J164980.1
501F161550.1
502K161550.1
511F155640.1
512L155640.1
521G144320.1
522H144320.1
531G167320.08
532I167320.08
541G166530.09
542J166530.09
551G160260.1
552K160260.1
561G154880.11
562L154880.11
571H144180.1
572I144180.1
581H145970.1
582J145970.1
591H150360.09
592K150360.09
601H148400.1
602L148400.1
611I165580.09
612J165580.09
621I159240.09
622K159240.09
631I154110.1
632L154110.1
641J159620.1
642K159620.1
651J155140.11
652L155140.11
661K157060.1
662L157060.1
LS refinement shellResolution: 3.033→3.112 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 1 -
Rwork0.45 22 -
all-23 -
obs--0.12 %

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