2GC4

Structural comparison of the oxidized ternary electron transfer complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans with the substrate-reduced, copper free complex at 1.9 A resolution.

> Summary

Summary for 2GC4

Related2MTA 2GC7
DescriptorMethylamine dehydrogenase heavy chain, Methylamine dehydrogenase light chain, Amicyanin, ... (8 entities in total)
Functional Keywordselectron transfer, methylamine dehydrogenase, cytochrome, blue copper protein, oxidoreductase, electron transport
Biological sourceParacoccus denitrificans
Cellular locationPeriplasm P29894 P22619 P22364
Periplasm (Potential) P29899
Total number of polymer chains16
Total molecular weight340575
Authors
Chen, Z.,Durley, R.,Davidson, V.L.,Mathews, F.S. (deposition date: 2006-03-13, release date: 2006-11-28, Last modification date: 2009-02-24)
Primary citation
Chen, Z.,Durley, R.,Davidson, V.L.,Mathews, F.S.
Structural comparison of the oxidized ternary electron transfer complex of methylamine dehydrogenase, amicyanin and cytochrome c551i from Paracoccus denitrificans with the substrate-reduced, copper free complex at 1.9 A resolution.
To be Published,
Experimental method
X-RAY DIFFRACTION (1.9 Å)
NMR Information
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.19260.3%3.4%4.4%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 2gc4
no rotation
Molmil generated image of 2gc4
rotated about x axis by 90°
Molmil generated image of 2gc4
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, E, I, MMethylamine dehydrogenase heavy chainpolymer38642449.74
UniProt (P29894)
Pfam (PF06433)
Paracoccus denitrificansMADH
B, F, J, NMethylamine dehydrogenase light chainpolymer13114210.84
UniProt (P22619)
Pfam (PF02975)
Paracoccus denitrificansMADH
C, G, K, OAmicyaninpolymer10511505.34
UniProt (P22364)
Pfam (PF00127)
Paracoccus denitrificans
D, H, L, PCytochrome c-Lpolymer14716275.04
UniProt (P29899)
Pfam (PF13442)
Paracoccus denitrificansCytochrome c551I, Cytochrome c552
COPPER (II) IONnon-polymer63.54
SODIUM IONnon-polymer23.04
PROTOPORPHYRIN IX CONTAINING FEnon-polymer616.54
waterwater18.01140

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains16
Total molecular weight337762.9
Non-Polymers*Number of molecules12
Total molecular weight2812.1
All*Total molecular weight340575.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.9 Å)

Cell axes81.368188.979128.836
Cell angles90.0099.7490.00
SpacegroupP 1 21 1
Resolution limits29.95 - 1.90
the highest resolution shell value2.020 - 1.900
R-work0.17300
the highest resolution shell value0.291
R-free0.19700
the highest resolution shell value0.311
RMSD bond length0.006
RMSD bond angle1.400

Data Collection Statistics

Resolution limits30.00 - 1.90
the highest resolution shell value -
Number of reflections254878
Rmerge_l_obs0.067
the highest resolution shell value0.329
Completeness84.1
Redundancy2.1
the highest resolution shell value1.9
I/sigma(I)0

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, SITTING DROP5.5295

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
C0042597cellular_componentperiplasmic space
C0005507molecular_functioncopper ion binding
C0009055molecular_functionelectron carrier activity
C0055114biological_processoxidation-reduction process
G0042597cellular_componentperiplasmic space
G0005507molecular_functioncopper ion binding
G0009055molecular_functionelectron carrier activity
G0055114biological_processoxidation-reduction process
K0042597cellular_componentperiplasmic space
K0005507molecular_functioncopper ion binding
K0009055molecular_functionelectron carrier activity
K0055114biological_processoxidation-reduction process
O0042597cellular_componentperiplasmic space
O0005507molecular_functioncopper ion binding
O0009055molecular_functionelectron carrier activity
O0055114biological_processoxidation-reduction process
D0042597cellular_componentperiplasmic space
D0009055molecular_functionelectron carrier activity
D0020037molecular_functionheme binding
D0005506molecular_functioniron ion binding
D0015945biological_processmethanol metabolic process
D0055114biological_processoxidation-reduction process
H0042597cellular_componentperiplasmic space
H0009055molecular_functionelectron carrier activity
H0020037molecular_functionheme binding
H0005506molecular_functioniron ion binding
H0015945biological_processmethanol metabolic process
H0055114biological_processoxidation-reduction process
L0042597cellular_componentperiplasmic space
L0009055molecular_functionelectron carrier activity
L0020037molecular_functionheme binding
L0005506molecular_functioniron ion binding
L0015945biological_processmethanol metabolic process
L0055114biological_processoxidation-reduction process
P0042597cellular_componentperiplasmic space
P0009055molecular_functionelectron carrier activity
P0020037molecular_functionheme binding
P0005506molecular_functioniron ion binding
P0015945biological_processmethanol metabolic process
P0055114biological_processoxidation-reduction process
A0042597cellular_componentperiplasmic space
A0030058molecular_functionamine dehydrogenase activity
A0052876molecular_functionmethylamine dehydrogenase (amicyanin) activity
A0030416biological_processmethylamine metabolic process
E0042597cellular_componentperiplasmic space
E0030058molecular_functionamine dehydrogenase activity
E0052876molecular_functionmethylamine dehydrogenase (amicyanin) activity
E0030416biological_processmethylamine metabolic process
I0042597cellular_componentperiplasmic space
I0030058molecular_functionamine dehydrogenase activity
I0052876molecular_functionmethylamine dehydrogenase (amicyanin) activity
I0030416biological_processmethylamine metabolic process
M0042597cellular_componentperiplasmic space
M0030058molecular_functionamine dehydrogenase activity
M0052876molecular_functionmethylamine dehydrogenase (amicyanin) activity
M0030416biological_processmethylamine metabolic process
B0030288cellular_componentouter membrane-bounded periplasmic space
B0030058molecular_functionamine dehydrogenase activity
B0052876molecular_functionmethylamine dehydrogenase (amicyanin) activity
B0009308biological_processamine metabolic process
F0030288cellular_componentouter membrane-bounded periplasmic space
F0030058molecular_functionamine dehydrogenase activity
F0052876molecular_functionmethylamine dehydrogenase (amicyanin) activity
F0009308biological_processamine metabolic process
J0030288cellular_componentouter membrane-bounded periplasmic space
J0030058molecular_functionamine dehydrogenase activity
J0052876molecular_functionmethylamine dehydrogenase (amicyanin) activity
J0009308biological_processamine metabolic process
N0030288cellular_componentouter membrane-bounded periplasmic space
N0030058molecular_functionamine dehydrogenase activity
N0052876molecular_functionmethylamine dehydrogenase (amicyanin) activity
N0009308biological_processamine metabolic process
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC14BINDING SITE FOR RESIDUE CU G 107
ChainResidue
GHIS53
GCYS92
GHIS95
GMET98

AC24BINDING SITE FOR RESIDUE CU K 107
ChainResidue
KHIS53
KCYS92
KHIS95
KMET98

AC34BINDING SITE FOR RESIDUE CU O 107
ChainResidue
OHIS53
OCYS92
OHIS95
OMET98

AC44BINDING SITE FOR RESIDUE CU C 107
ChainResidue
CHIS53
CCYS92
CHIS95
CMET98

AC56BINDING SITE FOR RESIDUE NA L 601
ChainResidue
KGLU31
LGLY72
LASP75
LTYR77
LHOH1056
LHOH1513

AC67BINDING SITE FOR RESIDUE NA P 602
ChainResidue
OGLU31
PGLY72
PASP75
PTYR77
PHOH1246
PHOH1495
PHOH2138

AC77BINDING SITE FOR RESIDUE NA H 603
ChainResidue
GGLU31
HGLY72
HASP75
HTYR77
HHOH1083
HHOH1553
HHOH1763

AC87BINDING SITE FOR RESIDUE NA D 604
ChainResidue
CHOH2139
DGLY72
DASP75
DTYR77
DHOH1001
DHOH2053
DHOH2140

AC917BINDING SITE FOR RESIDUE HEM H 200
ChainResidue
HMET56
HCYS57
HCYS60
HHIS61
HPRO71
HLEU73
HTRP78
HTHR79
HTYR80
HASN83
HLEU89
HLEU93
HALA97
HTHR98
HGLN100
HMET101
HHOH1763

BC116BINDING SITE FOR RESIDUE HEM L 200
ChainResidue
LMET56
LCYS57
LCYS60
LHIS61
LPRO71
LLEU73
LTRP78
LTHR79
LTYR80
LASN83
LLEU89
LALA97
LTHR98
LGLN100
LMET101
LHOH1513

BC217BINDING SITE FOR RESIDUE HEM D 200
ChainResidue
DMET56
DCYS57
DCYS60
DHIS61
DPRO71
DLEU73
DTRP78
DTHR79
DTYR80
DASN83
DLEU89
DLEU93
DALA97
DTHR98
DGLN100
DMET101
DHOH2053

BC316BINDING SITE FOR RESIDUE HEM P 200
ChainResidue
PMET56
PCYS57
PCYS60
PHIS61
PPRO71
PLEU73
PTRP78
PTHR79
PTYR80
PASN83
PLEU93
PALA97
PTHR98
PGLN100
PMET101
PHOH2138

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
HEM_2gc4_D_20025PROTOPORPHYRIN IX CONTAINING FE binding site
ChainResidueligand
DTYR53HEM: PROTOPORPHYRIN IX CONTAINING FE
DMET56-CYS57HEM: PROTOPORPHYRIN IX CONTAINING FE
DCYS60-HIS61HEM: PROTOPORPHYRIN IX CONTAINING FE
DGLY70-LEU73HEM: PROTOPORPHYRIN IX CONTAINING FE
DTYR77-TYR80HEM: PROTOPORPHYRIN IX CONTAINING FE
DASN83HEM: PROTOPORPHYRIN IX CONTAINING FE
DLEU89HEM: PROTOPORPHYRIN IX CONTAINING FE
DTHR92-LEU93HEM: PROTOPORPHYRIN IX CONTAINING FE
DALA97-THR98HEM: PROTOPORPHYRIN IX CONTAINING FE
DGLN100-MET101HEM: PROTOPORPHYRIN IX CONTAINING FE
DMET104HEM: PROTOPORPHYRIN IX CONTAINING FE
DLEU108HEM: PROTOPORPHYRIN IX CONTAINING FE
DTHR116HEM: PROTOPORPHYRIN IX CONTAINING FE
DVAL120HEM: PROTOPORPHYRIN IX CONTAINING FE

HEM_2gc4_H_20026PROTOPORPHYRIN IX CONTAINING FE binding site
ChainResidueligand
HTYR53HEM: PROTOPORPHYRIN IX CONTAINING FE
HMET56-CYS57HEM: PROTOPORPHYRIN IX CONTAINING FE
HCYS60-HIS61HEM: PROTOPORPHYRIN IX CONTAINING FE
HILE69-LEU73HEM: PROTOPORPHYRIN IX CONTAINING FE
HTYR77-TYR80HEM: PROTOPORPHYRIN IX CONTAINING FE
HASN83HEM: PROTOPORPHYRIN IX CONTAINING FE
HLEU89HEM: PROTOPORPHYRIN IX CONTAINING FE
HTHR92-LEU93HEM: PROTOPORPHYRIN IX CONTAINING FE
HALA97-THR98HEM: PROTOPORPHYRIN IX CONTAINING FE
HGLN100-MET101HEM: PROTOPORPHYRIN IX CONTAINING FE
HMET104HEM: PROTOPORPHYRIN IX CONTAINING FE
HLEU108HEM: PROTOPORPHYRIN IX CONTAINING FE
HTHR116HEM: PROTOPORPHYRIN IX CONTAINING FE
HVAL120HEM: PROTOPORPHYRIN IX CONTAINING FE

HEM_2gc4_L_20026PROTOPORPHYRIN IX CONTAINING FE binding site
ChainResidueligand
LTYR53HEM: PROTOPORPHYRIN IX CONTAINING FE
LMET56-CYS57HEM: PROTOPORPHYRIN IX CONTAINING FE
LCYS60-HIS61HEM: PROTOPORPHYRIN IX CONTAINING FE
LILE69-LEU73HEM: PROTOPORPHYRIN IX CONTAINING FE
LTYR77-TYR80HEM: PROTOPORPHYRIN IX CONTAINING FE
LASN83HEM: PROTOPORPHYRIN IX CONTAINING FE
LLEU89HEM: PROTOPORPHYRIN IX CONTAINING FE
LTHR92-LEU93HEM: PROTOPORPHYRIN IX CONTAINING FE
LALA97-THR98HEM: PROTOPORPHYRIN IX CONTAINING FE
LGLN100-MET101HEM: PROTOPORPHYRIN IX CONTAINING FE
LMET104HEM: PROTOPORPHYRIN IX CONTAINING FE
LLEU108HEM: PROTOPORPHYRIN IX CONTAINING FE
LTHR116HEM: PROTOPORPHYRIN IX CONTAINING FE
LVAL120HEM: PROTOPORPHYRIN IX CONTAINING FE

HEM_2gc4_P_20027PROTOPORPHYRIN IX CONTAINING FE binding site
ChainResidueligand
PILE8HEM: PROTOPORPHYRIN IX CONTAINING FE
PTYR53HEM: PROTOPORPHYRIN IX CONTAINING FE
PMET56-CYS57HEM: PROTOPORPHYRIN IX CONTAINING FE
PCYS60-HIS61HEM: PROTOPORPHYRIN IX CONTAINING FE
PILE69-LEU73HEM: PROTOPORPHYRIN IX CONTAINING FE
PTYR77-TYR80HEM: PROTOPORPHYRIN IX CONTAINING FE
PASN83HEM: PROTOPORPHYRIN IX CONTAINING FE
PLEU89HEM: PROTOPORPHYRIN IX CONTAINING FE
PTHR92-LEU93HEM: PROTOPORPHYRIN IX CONTAINING FE
PALA97-THR98HEM: PROTOPORPHYRIN IX CONTAINING FE
PGLN100-MET101HEM: PROTOPORPHYRIN IX CONTAINING FE
PMET104HEM: PROTOPORPHYRIN IX CONTAINING FE
PLEU108HEM: PROTOPORPHYRIN IX CONTAINING FE
PTHR116HEM: PROTOPORPHYRIN IX CONTAINING FE
PVAL120HEM: PROTOPORPHYRIN IX CONTAINING FE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI32Heme (covalent).
ChainResidueDetails
DCYS57
DCYS60

SWS_FT_FI62Heme (covalent).
ChainResidueDetails
HCYS57
HCYS60

SWS_FT_FI92Heme (covalent).
ChainResidueDetails
LCYS57
LCYS60

SWS_FT_FI122Heme (covalent).
ChainResidueDetails
PCYS57
PCYS60

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
CSA15Annotated By Reference To The Literature 2bbk
ChainResidueDetails
BASP76
BTHR122
BASP32
BTYR119
BTRP108

CSA25Annotated By Reference To The Literature 2bbk
ChainResidueDetails
FASP76
FTHR122
FASP32
FTYR119
FTRP108

CSA35Annotated By Reference To The Literature 2bbk
ChainResidueDetails
JASP76
JTHR122
JASP32
JTYR119
JTRP108

CSA45Annotated By Reference To The Literature 2bbk
ChainResidueDetails
NASP76
NTHR122
NASP32
NTYR119
NTRP108

> Sequence Neighbor

> Downloads

Resources

File formatFile name (file size)
PDBallpdb2gc4.ent.gz (507.87 KB)
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all (no-compress)pdb2gc4.ent (2.05 MB)
header onlypdb2gc4.ent.gz (14.62 KB)
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PDBx/mmCIF2gc4.cif.gz (620.12 KB)
PDBMLall2gc4.xml.gz (961.39 KB)
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no-atom2gc4-noatom.xml.gz (110.2 KB)
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ext-atom2gc4-extatom.xml.gz (579.57 KB)
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PDBMLplusall2gc4-plus.xml.gz (965.65 KB)
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no-atom2gc4-plus-noatom.xml.gz (114.46 KB)
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add only2gc4-add.xml.gz (4.25 KB)
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RDF2gc4.rdf.gz (212.42 KB)
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Structure factorsr2gc4sf.ent.gz (2.01 MB)
Biological unit (PDB format)2gc4.pdb1.gz (131.59 KB) (A,B,C,D)
*author defined assembly, 4 molecule(s) (tetrameric)
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2gc4.pdb2.gz (131.75 KB) (E,F,G,H)
*author defined assembly, 4 molecule(s) (tetrameric)
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2gc4.pdb3.gz (133.18 KB) (I,J,K,L)
*author defined assembly, 4 molecule(s) (tetrameric)
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2gc4.pdb4.gz (133.21 KB) (M,N,O,P)
*author defined assembly, 4 molecule(s) (tetrameric)
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Validation reportsPDF2gc4​_validation.pdf.gz (573.14 KB)
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PDF-full2gc4​_full​_validation.pdf.gz (624.48 KB)
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XML2gc4​_validation.xml.gz (114.92 KB)
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PNG2gc4​_multipercentile​_validation.png.gz (139.22 KB)
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SVG2gc4​_multipercentile​_validation.svg.gz (948 B)
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Sequence (fasta)2gc4​_seq.txt
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