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(-) Description

Title :  CRYSTAL STRUCTURE OF OXIDIZED RECOMBINANT CYTOCHROME C4 FROM PSEUDOMONAS STUTZERI
 
Authors :  A. Noergaard, P. Harris, S. Larsen, H. E. M. Christensen
Date :  18 Jul 02  (Deposition) - 16 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Electron Transport, Diheme Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Noergaard, P. Harris, S. Larsen, H. E. M. Christensen
Structural Comparison Of Recombinant Pseudomonas Stutzeri Cytochrome C4 In Two Oxidation States
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME C4
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemPSEUDOMONAS PUTIDA
    Expression System PlasmidPNM185
    Expression System StrainPAW340
    Expression System Taxid303
    Expression System Vector TypePLASMID
    Organism ScientificPSEUDOMONAS STUTZERI
    Organism Taxid316

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HEC8Ligand/IonHEME C
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2HEC2Ligand/IonHEME C
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2HEC2Ligand/IonHEME C
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2HEC2Ligand/IonHEME C
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2HEC2Ligand/IonHEME C

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:13 , CYS A:14 , CYS A:17 , HIS A:18 , PHE A:29 , PRO A:30 , LEU A:32 , TYR A:39 , GLN A:43 , ILE A:47 , ARG A:61 , VAL A:63 , GLU A:65 , MET A:66 , MET A:69 , LEU A:70 , ILE A:81 , TYR A:145 , LYS A:148 , GLN A:149 , HEC A:200 , HOH A:204 , HOH A:232 , HOH A:316BINDING SITE FOR RESIDUE HEC A 199
2AC2SOFTWARETYR A:39 , LYS A:42 , GLN A:43 , ALA A:118 , CYS A:119 , CYS A:122 , HIS A:123 , PRO A:136 , LEU A:138 , TYR A:145 , GLN A:149 , ARG A:158 , ASN A:160 , ILE A:166 , MET A:167 , HEC A:199 , HOH A:202 , HOH A:272 , HOH A:341BINDING SITE FOR RESIDUE HEC A 200
3AC3SOFTWAREVAL B:13 , CYS B:14 , CYS B:17 , HIS B:18 , PHE B:29 , PRO B:30 , TYR B:39 , GLN B:43 , ILE B:47 , ARG B:61 , VAL B:63 , GLU B:65 , MET B:66 , MET B:69 , LEU B:70 , TYR B:145 , LYS B:148 , GLN B:149 , HEC B:200 , HOH B:203 , HOH B:219BINDING SITE FOR RESIDUE HEC B 199
4AC4SOFTWARETYR B:39 , LYS B:42 , GLN B:43 , ALA B:118 , CYS B:119 , CYS B:122 , HIS B:123 , PHE B:135 , PRO B:136 , LEU B:138 , TYR B:145 , ARG B:158 , ASN B:160 , ILE B:166 , MET B:167 , HEC B:199 , HOH B:201 , HOH B:340 , ALA D:16BINDING SITE FOR RESIDUE HEC B 200
5AC5SOFTWAREPHE A:135 , VAL C:13 , CYS C:14 , CYS C:17 , HIS C:18 , PHE C:29 , TYR C:39 , GLN C:43 , LEU C:44 , ILE C:47 , ARG C:61 , VAL C:63 , GLU C:65 , MET C:66 , MET C:69 , LEU C:70 , ILE C:81 , TYR C:145 , LYS C:148 , GLN C:149 , HEC C:200 , HOH C:201 , HOH C:273BINDING SITE FOR RESIDUE HEC C 199
6AC6SOFTWAREALA B:16 , TYR C:39 , LYS C:42 , GLN C:43 , ALA C:118 , CYS C:119 , CYS C:122 , HIS C:123 , PHE C:135 , PRO C:136 , LEU C:138 , TYR C:145 , ARG C:158 , ASN C:160 , MET C:167 , VAL C:170 , HEC C:199 , HOH C:204 , HOH C:219 , HOH C:223BINDING SITE FOR RESIDUE HEC C 200
7AC7SOFTWAREPHE B:135 , VAL D:13 , CYS D:14 , CYS D:17 , HIS D:18 , PHE D:29 , PRO D:30 , TYR D:39 , GLN D:43 , LEU D:44 , ILE D:47 , ARG D:61 , VAL D:63 , GLU D:65 , MET D:66 , MET D:69 , LEU D:70 , ILE D:81 , TYR D:145 , LYS D:148 , GLN D:149 , HEC D:200 , HOH D:201 , HOH D:243 , HOH D:294BINDING SITE FOR RESIDUE HEC D 199
8AC8SOFTWAREALA A:16 , TYR D:39 , LYS D:42 , GLN D:43 , ALA D:118 , CYS D:119 , CYS D:122 , HIS D:123 , PHE D:135 , PRO D:136 , LEU D:138 , TYR D:145 , GLN D:149 , ARG D:158 , ASN D:160 , ILE D:166 , MET D:167 , VAL D:170 , HEC D:199 , HOH D:202 , HOH D:225 , HOH D:247BINDING SITE FOR RESIDUE HEC D 200
9AC9SOFTWAREGLY A:188 , LEU A:189 , HIS A:190 , HOH A:205 , HOH A:225BINDING SITE FOR RESIDUE GOL A 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1M70)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1M70)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1M70)

(-) PROSITE Motifs  (1, 8)

Asymmetric Unit (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC4_PSEST22-109
 
 
 
118-210
 
 
 
  8A:2-89
B:2-89
C:2-89
D:2-89
A:98-190
B:98-190
C:98-190
D:98-190
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC4_PSEST22-109
 
 
 
118-210
 
 
 
  2A:2-89
-
-
-
A:98-190
-
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC4_PSEST22-109
 
 
 
118-210
 
 
 
  2-
B:2-89
-
-
-
B:98-190
-
-
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC4_PSEST22-109
 
 
 
118-210
 
 
 
  2-
-
C:2-89
-
-
-
C:98-190
-
Biological Unit 4 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTCPS51007 Cytochrome c family profile.CYC4_PSEST22-109
 
 
 
118-210
 
 
 
  2-
-
-
D:2-89
-
-
-
D:98-190

(-) Exons   (0, 0)

(no "Exon" information available for 1M70)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:190
 aligned with CYC4_PSEST | Q52369 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:190
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
           CYC4_PSEST    21 AGDAEAGQGKVAVCGACHGVDGNSPAPNFPKLAGQGERYLLKQLQDIKAGSTPGAPEGVGRKVLEMTGMLDPLSDQDLEDIAAYFSSQKGSVGYADPALAKQGEKLFRGGKLDQGMPACTGCHAPNGVGNDLAGFPKLGGQHAAYTAKQLTDFREGNRTNDGDTMIMRGVAAKLSNKDIEALSSYIQGLH 210
               SCOP domains d1m70a1 A:1-92 Cytochrome c4                                                                d1m70a2 A:93-190 Cytochrome c4                                                                     SCOP domains
               CATH domains 1m70A01 A:1-91 Cytochrome c                                                                1m70A02 A:92-190 Cytochrome c                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh..........hhhhh......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...hhhhhh.....hhhhh.......hhhhhhhhhhhhhh.........hhhhhhhh..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: A:2-89 UniProt: 22-109                                                       --------CYTC  PDB: A:98-190 UniProt: 118-210                                                          PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m70 A   1 AGDAEAGQGKVAVCGACHGVDGNSPAPNFPKLAGQGERYLLKQLQDIKAGSTPGAPEGVGRKVLEMTGMLDPLSDQDLEDIAAYFSSQKGSVGYADPALAKQGEKLFRGGKLDQGMPACTGCHAPNGVGNDLAGFPKLGGQHAAYTAKQLTDFREGNRTNDGDTMIMRGVAAKLSNKDIEALSSYIQGLH 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain B from PDB  Type:PROTEIN  Length:190
 aligned with CYC4_PSEST | Q52369 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:190
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
           CYC4_PSEST    21 AGDAEAGQGKVAVCGACHGVDGNSPAPNFPKLAGQGERYLLKQLQDIKAGSTPGAPEGVGRKVLEMTGMLDPLSDQDLEDIAAYFSSQKGSVGYADPALAKQGEKLFRGGKLDQGMPACTGCHAPNGVGNDLAGFPKLGGQHAAYTAKQLTDFREGNRTNDGDTMIMRGVAAKLSNKDIEALSSYIQGLH 210
               SCOP domains d1m70b1 B:1-92 Cytochrome c4                                                                d1m70b2 B:93-190 Cytochrome c4                                                                     SCOP domains
               CATH domains 1m70B01 B:1-91 Cytochrome c                                                                1m70B02 B:92-190 Cytochrome c                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh..........hhhhh......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...hhhhhh.................hhhhhhhhhhhhhh.........hhhhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: B:2-89 UniProt: 22-109                                                       --------CYTC  PDB: B:98-190 UniProt: 118-210                                                          PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m70 B   1 AGDAEAGQGKVAVCGACHGVDGNSPAPNFPKLAGQGERYLLKQLQDIKAGSTPGAPEGVGRKVLEMTGMLDPLSDQDLEDIAAYFSSQKGSVGYADPALAKQGEKLFRGGKLDQGMPACTGCHAPNGVGNDLAGFPKLGGQHAAYTAKQLTDFREGNRTNDGDTMIMRGVAAKLSNKDIEALSSYIQGLH 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain C from PDB  Type:PROTEIN  Length:190
 aligned with CYC4_PSEST | Q52369 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:190
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
           CYC4_PSEST    21 AGDAEAGQGKVAVCGACHGVDGNSPAPNFPKLAGQGERYLLKQLQDIKAGSTPGAPEGVGRKVLEMTGMLDPLSDQDLEDIAAYFSSQKGSVGYADPALAKQGEKLFRGGKLDQGMPACTGCHAPNGVGNDLAGFPKLGGQHAAYTAKQLTDFREGNRTNDGDTMIMRGVAAKLSNKDIEALSSYIQGLH 210
               SCOP domains d1m70c1 C:1-92 Cytochrome c4                                                                d1m70c2 C:93-190 Cytochrome c4                                                                     SCOP domains
               CATH domains 1m70C01 C:1-91 Cytochrome c                                                                1m70C02 C:92-190 Cytochrome c                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh..hhhhhhhhh................hhhhhhhhhhhhhhhhh..........hhhhh......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...hhhhhh.....hhhhh.......hhhhhhhhhhhhhh.........hhhhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: C:2-89 UniProt: 22-109                                                       --------CYTC  PDB: C:98-190 UniProt: 118-210                                                          PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m70 C   1 AGDAEAGQGKVAVCGACHGVDGNSPAPNFPKLAGQGERYLLKQLQDIKAGSTPGAPEGVGRKVLEMTGMLDPLSDQDLEDIAAYFSSQKGSVGYADPALAKQGEKLFRGGKLDQGMPACTGCHAPNGVGNDLAGFPKLGGQHAAYTAKQLTDFREGNRTNDGDTMIMRGVAAKLSNKDIEALSSYIQGLH 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

Chain D from PDB  Type:PROTEIN  Length:190
 aligned with CYC4_PSEST | Q52369 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:190
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
           CYC4_PSEST    21 AGDAEAGQGKVAVCGACHGVDGNSPAPNFPKLAGQGERYLLKQLQDIKAGSTPGAPEGVGRKVLEMTGMLDPLSDQDLEDIAAYFSSQKGSVGYADPALAKQGEKLFRGGKLDQGMPACTGCHAPNGVGNDLAGFPKLGGQHAAYTAKQLTDFREGNRTNDGDTMIMRGVAAKLSNKDIEALSSYIQGLH 210
               SCOP domains d1m70d1 D:1-92 Cytochrome c4                                                                d1m70d2 D:93-190 Cytochrome c4                                                                     SCOP domains
               CATH domains 1m70D01 D:1-91 Cytochrome c                                                                1m70D02 D:92-190 Cytochrome c                                                                       CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------Cytochrom_C-1m70D01 D:100-190                                                               Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------Cytochrom_C-1m70D02 D:100-190                                                               Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------Cytochrom_C-1m70D03 D:100-190                                                               Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------Cytochrom_C-1m70D04 D:100-190                                                               Pfam domains (4)
           Pfam domains (5) ---------------------------------------------------------------------------------------------------Cytochrom_C-1m70D05 D:100-190                                                               Pfam domains (5)
           Pfam domains (6) ---------------------------------------------------------------------------------------------------Cytochrom_C-1m70D06 D:100-190                                                               Pfam domains (6)
           Pfam domains (7) ---------------------------------------------------------------------------------------------------Cytochrom_C-1m70D07 D:100-190                                                               Pfam domains (7)
           Pfam domains (8) ---------------------------------------------------------------------------------------------------Cytochrom_C-1m70D08 D:100-190                                                               Pfam domains (8)
         Sec.struct. author ..hhhhhhh.hhhhhhhhh................hhhhhhhhhhhhhhhhh..........hhhhh......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh...hhhhhh.....hhhhh.......hhhhhhhhhhhhhh.........hhhhhhhh..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -CYTC  PDB: D:2-89 UniProt: 22-109                                                       --------CYTC  PDB: D:98-190 UniProt: 118-210                                                          PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m70 D   1 AGDAEAGQGKVAVCGACHGVDGNSPAPNFPKLAGQGERYLLKQLQDIKAGSTPGAPEGVGRKVLEMTGMLDPLSDQDLEDIAAYFSSQKGSVGYADPALAKQGEKLFRGGKLDQGMPACTGCHAPNGVGNDLAGFPKLGGQHAAYTAKQLTDFREGNRTNDGDTMIMRGVAAKLSNKDIEALSSYIQGLH 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 8)

Asymmetric Unit

(-) CATH Domains  (1, 8)

Asymmetric Unit

(-) Pfam Domains  (1, 8)

Asymmetric Unit

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CYC4_PSEST | Q52369)
molecular function
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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  1m70
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CYC4_PSEST | Q523691etp 1m6z

(-) Related Entries Specified in the PDB File

1etp 1ETP CONTAINS THE NATIVE PROTEIN WITHOUT VERIFICATION OF OXIDATION STATE
1m6z 1M6Z CONTAINS THE REDUCED RECOMBINANT CYTOCHROME C4