HEADER ELECTRON TRANSPORT 02-APR-02 1J5C TITLE SOLUTION STRUCTURE OF OXIDIZED PARAMAGNETIC CU(II) PLASTOCYANIN FROM TITLE 2 SYNECHOCYSTIS PCC6803 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLASTOCYANIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCYSTIS SP. PCC 6803; SOURCE 3 ORGANISM_TAXID: 1148; SOURCE 4 STRAIN: PCC6803; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BLR(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET3D KEYWDS COPPER PROTEIN BETA BARREL ELECTRON TRANSFER, ELECTRON TRANSPORT EXPDTA SOLUTION NMR NUMMDL 35 AUTHOR I.BERTINI,S.CIURLI,A.DIKIY,C.O.FERNANDEZ,C.LUCHINAT,N.SAFAROV, AUTHOR 2 S.SHUMILIN,A.J.VILA REVDAT 3 27-OCT-21 1J5C 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1J5C 1 VERSN REVDAT 1 10-APR-02 1J5C 0 SPRSDE 10-APR-02 1J5C 1I0W JRNL AUTH I.BERTINI,S.CIURLI,A.DIKIY,C.O.FERNANDEZ,C.LUCHINAT, JRNL AUTH 2 N.SAFAROV,S.SHUMILIN,A.J.VILA JRNL TITL THE FIRST SOLUTION STRUCTURE OF A PARAMAGNETIC COPPER(II) JRNL TITL 2 PROTEIN: THE CASE OF OXIDIZED PLASTOCYANIN FROM THE JRNL TITL 3 CYANOBACTERIUM SYNECHOCYSTIS PCC6803. JRNL REF J.AM.CHEM.SOC. V. 123 2405 2001 JRNL REFN ISSN 0002-7863 JRNL PMID 11456890 JRNL DOI 10.1021/JA0033685 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.0, DYANA 1.5 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUENTERT (DYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE PROTEIN CONTAINS PARAMAGNETIC REMARK 3 COPPER(II), WHOSE ELECTRONIC RELAXATION TIMES ARE QUITE REMARK 3 UNFAVORABLE FOR NMR SOLUTION STUDIES. THE STRUCTURE HAS BEEN REMARK 3 SOLVED ON THE BASIS OF 1041 MEANINGFUL NOESY CROSS PEAKS, 18 1D REMARK 3 NOES, 26 T1 VALUES, 96 DIHEDRAL ANGLE CONSTRAINTS AND 18 H- REMARK 3 BONDS. THE DETECTION OF BROAD HYPERFINE SHIFTED SIGNALS AND REMARK 3 THEIR FULL ASSIGNMENT ALLOWED THE IDENTIFICATION OF THE REMARK 3 COPPER(II) LIGANDS AND THE DETERMINATION OF THE CU-S-C-H REMARK 3 DIHEDRAL ANGLE FOR THE COORDINATED CYSTEINE. THE GLOBAL ROOT REMARK 3 MEAN SQUARE DEVIATION FROM THE MEAN STRUCTURE FOR THE SOLUTION REMARK 3 STRUCTURE FAMILY IS 0.72 AND 1.16 FOR BACKBONE AND HEAVY ATOMS, REMARK 3 RESPECTIVELY. REMARK 4 REMARK 4 1J5C COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-02. REMARK 100 THE DEPOSITION ID IS D_1000001631. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 5.2 REMARK 210 IONIC STRENGTH : 50 MM PHOSPHATE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 3 MM PLASTOCYANIN U-15N 50 MM REMARK 210 PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; HNHA; PROTON T1 (HSQC) REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.0, XEASY 1.3.13 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 35 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HE3 MET A 91 CU CU A 99 0.85 REMARK 500 CE MET A 91 CU CU A 99 1.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 LEU A 14 -63.05 -98.25 REMARK 500 1 LYS A 35 -164.70 -177.40 REMARK 500 1 LEU A 36 70.28 65.56 REMARK 500 1 ALA A 45 79.12 -111.35 REMARK 500 1 ASP A 46 -73.14 -95.98 REMARK 500 1 LYS A 59 36.37 -97.36 REMARK 500 1 LEU A 61 107.38 -175.35 REMARK 500 1 PHE A 63 -55.58 -123.15 REMARK 500 1 PRO A 85 -88.81 -75.00 REMARK 500 1 HIS A 86 -164.62 52.09 REMARK 500 1 ARG A 87 55.16 -160.86 REMARK 500 2 LYS A 35 -166.54 -174.96 REMARK 500 2 LEU A 36 61.01 65.74 REMARK 500 2 ASP A 46 -65.47 -99.42 REMARK 500 2 ASP A 49 -179.38 -68.23 REMARK 500 2 PHE A 63 -60.41 -141.41 REMARK 500 2 ARG A 87 79.77 -119.83 REMARK 500 2 ALA A 89 88.49 172.94 REMARK 500 2 MET A 91 90.75 58.85 REMARK 500 2 VAL A 92 -58.22 -137.80 REMARK 500 3 LEU A 36 68.76 63.93 REMARK 500 3 HIS A 39 132.20 -176.60 REMARK 500 3 ALA A 45 79.90 -107.25 REMARK 500 3 ASP A 46 -74.04 -95.99 REMARK 500 3 ALA A 50 -70.10 -73.77 REMARK 500 3 LEU A 61 34.49 -172.97 REMARK 500 3 PHE A 63 -49.38 -158.61 REMARK 500 3 PRO A 85 -86.31 -74.96 REMARK 500 3 HIS A 86 -167.65 66.15 REMARK 500 3 ALA A 89 -76.67 -145.09 REMARK 500 4 SER A 11 42.42 -88.40 REMARK 500 4 LYS A 35 -166.97 -174.78 REMARK 500 4 LEU A 36 70.30 64.34 REMARK 500 4 HIS A 39 145.70 60.48 REMARK 500 4 ALA A 45 78.31 -111.78 REMARK 500 4 ASP A 46 -68.26 -92.48 REMARK 500 4 ASP A 49 174.97 -58.99 REMARK 500 4 ALA A 50 -70.28 -80.07 REMARK 500 4 PHE A 63 -47.36 -144.32 REMARK 500 4 ALA A 89 -55.92 -125.39 REMARK 500 4 VAL A 92 -76.68 -151.21 REMARK 500 5 LEU A 14 53.52 -91.97 REMARK 500 5 LEU A 36 68.33 65.55 REMARK 500 5 PRO A 38 -169.01 -74.97 REMARK 500 5 ALA A 45 73.49 -118.59 REMARK 500 5 ASP A 46 -83.87 -92.00 REMARK 500 5 LEU A 61 38.09 -171.74 REMARK 500 5 PHE A 63 -47.26 -156.13 REMARK 500 5 ALA A 65 101.41 -47.10 REMARK 500 5 CYS A 83 61.85 -108.11 REMARK 500 REMARK 500 THIS ENTRY HAS 394 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 99 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 39 ND1 REMARK 620 2 CYS A 83 SG 96.9 REMARK 620 3 HIS A 86 ND1 112.5 79.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 99 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1J5D RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF OXIDIZED PARAMAGNETIC CU(II) PLASTOCYANIN REMARK 900 FROM SYNECHOCYSTIS PCC6803-MINIMIZED AVERAGE STRUCTURE DBREF 1J5C A 1 98 UNP P21697 PLAS_SYNY3 29 126 SEQADV 1J5C ASP A 98 UNP P21697 GLU 126 ENGINEERED MUTATION SEQRES 1 A 98 ALA ASN ALA THR VAL LYS MET GLY SER ASP SER GLY ALA SEQRES 2 A 98 LEU VAL PHE GLU PRO SER THR VAL THR ILE LYS ALA GLY SEQRES 3 A 98 GLU GLU VAL LYS TRP VAL ASN ASN LYS LEU SER PRO HIS SEQRES 4 A 98 ASN ILE VAL PHE ALA ALA ASP GLY VAL ASP ALA ASP THR SEQRES 5 A 98 ALA ALA LYS LEU SER HIS LYS GLY LEU ALA PHE ALA ALA SEQRES 6 A 98 GLY GLU SER PHE THR SER THR PHE THR GLU PRO GLY THR SEQRES 7 A 98 TYR THR TYR TYR CYS GLU PRO HIS ARG GLY ALA GLY MET SEQRES 8 A 98 VAL GLY LYS VAL VAL VAL ASP HET CU A 99 1 HETNAM CU COPPER (II) ION FORMUL 2 CU CU 2+ HELIX 1 1 ASP A 49 SER A 57 1 9 SHEET 1 A 3 ALA A 3 THR A 4 0 SHEET 2 A 3 GLU A 28 TRP A 31 1 O GLU A 28 N ALA A 3 SHEET 3 A 3 PHE A 69 THR A 72 -1 O PHE A 69 N TRP A 31 SHEET 1 B 2 THR A 20 LYS A 24 0 SHEET 2 B 2 LYS A 94 ASP A 98 1 O LYS A 94 N VAL A 21 SHEET 1 C 2 PHE A 43 ALA A 44 0 SHEET 2 C 2 THR A 80 TYR A 81 -1 O THR A 80 N ALA A 44 LINK ND1 HIS A 39 CU CU A 99 1555 1555 2.32 LINK SG CYS A 83 CU CU A 99 1555 1555 2.42 LINK ND1 HIS A 86 CU CU A 99 1555 1555 2.31 CISPEP 1 GLU A 17 PRO A 18 1 0.09 CISPEP 2 SER A 37 PRO A 38 1 0.00 CISPEP 3 GLU A 17 PRO A 18 2 0.17 CISPEP 4 SER A 37 PRO A 38 2 0.02 CISPEP 5 GLU A 17 PRO A 18 3 -0.03 CISPEP 6 SER A 37 PRO A 38 3 0.04 CISPEP 7 GLU A 17 PRO A 18 4 0.01 CISPEP 8 SER A 37 PRO A 38 4 0.01 CISPEP 9 GLU A 17 PRO A 18 5 0.02 CISPEP 10 SER A 37 PRO A 38 5 0.03 CISPEP 11 GLU A 17 PRO A 18 6 -0.02 CISPEP 12 SER A 37 PRO A 38 6 0.11 CISPEP 13 GLU A 17 PRO A 18 7 0.01 CISPEP 14 SER A 37 PRO A 38 7 0.13 CISPEP 15 GLU A 17 PRO A 18 8 0.00 CISPEP 16 SER A 37 PRO A 38 8 0.12 CISPEP 17 GLU A 17 PRO A 18 9 -0.14 CISPEP 18 SER A 37 PRO A 38 9 0.07 CISPEP 19 GLU A 17 PRO A 18 10 0.06 CISPEP 20 SER A 37 PRO A 38 10 -0.05 CISPEP 21 GLU A 17 PRO A 18 11 0.03 CISPEP 22 SER A 37 PRO A 38 11 -0.01 CISPEP 23 GLU A 17 PRO A 18 12 0.03 CISPEP 24 SER A 37 PRO A 38 12 0.08 CISPEP 25 GLU A 17 PRO A 18 13 0.01 CISPEP 26 SER A 37 PRO A 38 13 0.05 CISPEP 27 GLU A 17 PRO A 18 14 0.01 CISPEP 28 SER A 37 PRO A 38 14 0.08 CISPEP 29 GLU A 17 PRO A 18 15 -0.04 CISPEP 30 SER A 37 PRO A 38 15 0.08 CISPEP 31 GLU A 17 PRO A 18 16 -0.08 CISPEP 32 SER A 37 PRO A 38 16 -0.11 CISPEP 33 GLU A 17 PRO A 18 17 -0.01 CISPEP 34 SER A 37 PRO A 38 17 -0.07 CISPEP 35 GLU A 17 PRO A 18 18 -0.01 CISPEP 36 SER A 37 PRO A 38 18 -0.07 CISPEP 37 GLU A 17 PRO A 18 19 -0.03 CISPEP 38 SER A 37 PRO A 38 19 0.10 CISPEP 39 GLU A 17 PRO A 18 20 -0.05 CISPEP 40 SER A 37 PRO A 38 20 -0.04 CISPEP 41 GLU A 17 PRO A 18 21 -0.05 CISPEP 42 SER A 37 PRO A 38 21 0.01 CISPEP 43 GLU A 17 PRO A 18 22 -0.01 CISPEP 44 SER A 37 PRO A 38 22 0.04 CISPEP 45 GLU A 17 PRO A 18 23 0.03 CISPEP 46 SER A 37 PRO A 38 23 -0.06 CISPEP 47 GLU A 17 PRO A 18 24 0.10 CISPEP 48 SER A 37 PRO A 38 24 0.07 CISPEP 49 GLU A 17 PRO A 18 25 -0.06 CISPEP 50 SER A 37 PRO A 38 25 0.03 CISPEP 51 GLU A 17 PRO A 18 26 -0.03 CISPEP 52 SER A 37 PRO A 38 26 -0.07 CISPEP 53 GLU A 17 PRO A 18 27 0.01 CISPEP 54 SER A 37 PRO A 38 27 0.06 CISPEP 55 GLU A 17 PRO A 18 28 0.09 CISPEP 56 SER A 37 PRO A 38 28 -0.15 CISPEP 57 GLU A 17 PRO A 18 29 -0.07 CISPEP 58 SER A 37 PRO A 38 29 0.15 CISPEP 59 GLU A 17 PRO A 18 30 0.04 CISPEP 60 SER A 37 PRO A 38 30 -0.09 CISPEP 61 GLU A 17 PRO A 18 31 0.09 CISPEP 62 SER A 37 PRO A 38 31 0.08 CISPEP 63 GLU A 17 PRO A 18 32 0.04 CISPEP 64 SER A 37 PRO A 38 32 -0.01 CISPEP 65 GLU A 17 PRO A 18 33 0.03 CISPEP 66 SER A 37 PRO A 38 33 -0.02 CISPEP 67 GLU A 17 PRO A 18 34 -0.01 CISPEP 68 SER A 37 PRO A 38 34 -0.01 CISPEP 69 GLU A 17 PRO A 18 35 -0.06 CISPEP 70 SER A 37 PRO A 38 35 -0.16 SITE 1 AC1 5 PHE A 16 HIS A 39 CYS A 83 HIS A 86 SITE 2 AC1 5 MET A 91 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20 MODEL 21 MODEL 22 MODEL 23 MODEL 24 MODEL 25 MODEL 26 MODEL 27 MODEL 28 MODEL 29 MODEL 30 MODEL 31 MODEL 32 MODEL 33 MODEL 34 MODEL 35