HEADER ELECTRON TRANSPORT 30-JAN-01 1I0Y OBSLTE 10-APR-02 1I0Y 1J5D TITLE SOLUTION STRUCTURE OF OXIDIZED PARAMAGNETIC CU(II) TITLE 2 PLASTOCYANIN FROM SYNECHOCYSTIS PCC6803-MINIMIZED AVERAGE TITLE 3 STRUCTURE 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.; SOURCE 3 ORGANISM_COMMON: BACTERIA; SOURCE 4 STRAIN: PCC6803; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: BACTERIA; 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 EXPDTA NMR AUTHOR I.BERTINI,S.CIURLI,A.DIKIY,C.O.FERNANDEZ,C.LUCHINAT, AUTHOR 2 N.SAFAROV,S.SHUMILIN,A.J.VILA REVDAT 2 10-APR-02 1I0Y 1 OBSLTE REVDAT 1 14-FEB-01 1I0Y 0 JRNL AUTH I.BERTINI,S.CIURLI,A.DIKIY,C.O.FERNANDEZ, JRNL AUTH 2 C.LUCHINAT,N.SAFAROV,S.SHUMILIN,A.J.VILA JRNL TITL THE FIRST SOLUTION STRUCTURE OF A PARAMAGNETIC JRNL TITL 2 COPPER(II) PROTEIN: THE CASE OF OXIDIZED JRNL TITL 3 PLASTOCYANIN FROM THE CYANOBACTERIUM SYNECHOCYSTIS JRNL TITL 4 PCC6803 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, AMBER 5.0 REMARK 3 AUTHORS : GUENTERT (DYANA), KOLLMAN (AMBER) 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 REMARK 3 1D 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 REMARK 3 ATOMS, RESPECTIVELY. THE MEAN STRUCTURE FROM THE DYANA FAMILY REMARK 3 WAS CALCULATED USING MOLMOL AND SUBJECTED TO RESTRAINED ENERGY REMARK 3 MINIMIZATION (REM) USING THE SANDER MODULE OF THE AMBER 5.0 REMARK 3 PROGRAM PACKAGE. THE FORCE FIELD PARAMETERS FOR ALL RESIDUES, REMARK 3 EXCLUDED THOSE FOR THE COPPER-COORDINATED LIGANDS, WERE THE REMARK 3 STANDARD AMBER "ALL-ATOMS" PARAMETERS. THE CALCULATIONS WERE REMARK 3 PERFORMED IN VACUO WITH THE DISTANCE-DEPENDENT DIELECTRIC REMARK 3 CONSTANT OPTION. THE NON-BONDED INTERACTIONS WERE EVALUATED REMARK 3 WITH A CUT-OFF OF 10 A. THE MIXED LINEAR-HARMONIC FLAT- REMARK 3 BOTTOMED POTENTIAL IMPLEMENTED IN SANDER WAS APPLIED TO ALL REMARK 3 STRUCTURAL CONSTRAINTS. THIS POTENTIAL INVOLVES A NULL FORCE REMARK 3 CONSTANT FOR STRUCTURAL CONSTRAINTS WITHIN THE ALLOWED LIMITS, REMARK 3 A NON-ZERO HARMONIC FORCE CONSTANT IN A SMALL INTERVAL OUTSIDE REMARK 3 THE ALLOWED LIMITS, AND A LINEARLY DEPENDENT POTENTIAL BEYOND REMARK 3 THAT LIMIT. NOE-DERIVED DISTANCE CONSTRAINTS WERE RESTRICTED REMARK 3 BELOW THE UPPER DISTANCE LIMIT (RI), USING A FORCE CONSTANT OF REMARK 3 32 KCAL MOL-1 A-2 FOR THE INTERVAL RI+0.5 A. DISTANCE REMARK 3 CONSTRAINTS INVOLVING THE SAME H-BONDS USED FOR DYANA REMARK 3 CALCULATIONS WERE INCLUDED IN THE REM CALCULATION, RESTRICTING REMARK 3 THE NH...O AND N...O DISTANCES TO THE SAME UPPER (RI) VALUES REMARK 3 USED IN DYANA, WITH A FORCE CONSTANT OF 32 KCAL MOL-1 A-2 FOR REMARK 3 THE RANGE RI + 0.5 A. THE CU-H DISTANCES DERIVED FROM THE REMARK 3 ANALYSIS OF THE NON-SELECTIVE LONGITUDINAL RELAXATION RATES REMARK 3 WERE ALSO RESTRAINED TO THE SAME UPPER (RI) LIMITS USED IN REMARK 3 DYANA, WITH A FORCE CONSTANT OF 32 KCAL MOL-1 A-2 FOR RI + 0.5 REMARK 3 A. THE CU-NHIS AND CU-SCYS DISTANCES WERE CONSTRAINED AT 2.1+/ REMARK 3 -0.1 A AND 2.2+/-0.1 A, RESPECTIVELY, USING A LINEAR-HARMONIC REMARK 3 FLAT-BOTTOMED POTENTIAL WITH FORCE CONSTANTS OF 50 KCAL MOL-1 REMARK 3 A-2 IN THE 0.3-A DISTANCE RANGES BELOW AND ABOVE THESE LIMITS. REMARK 3 THE CU-SMET DISTANCE WAS ANALOGOUSLY CONSTRAINED WITHIN THE REMARK 3 2.75+/-0.05 A RANGE, USING A FORCE CONSTANT OF 40 KCAL MOL-1 A REMARK 3 -2. THE CU-N(HIS)-CG, CU-N(HIS)-CE, CU-S(CYS)-CB, CU-S(MET)- REMARK 3 CG, AND CU-S(MET)-CE ANGLES WERE RESTRAINED AROUND 127+/-0, REMARK 3 127+/-0, 105+/-5, 130+/-10, 110+/-10, RESPECTIVELY, USING A REMARK 3 LINEAR-HARMONIC FLAT-BOTTOMED POTENTIAL WITH FORCE CONSTANTS REMARK 3 OF 50 KCAL MOL-1 DEG-2 IN THE 50 RANGES BELOW AND ABOVE THE REMARK 3 GIVEN VALUES. ANALOGOUSLY, THE (HIS)N-CU-N(HIS), (HIS)N-CU- REMARK 3 S(CYS), (HIS)N-CU-S(MET), AND (MET)S-CU-S(CYS) ANGLES WERE REMARK 3 RESTRAINED IN THE 110+/-10, 125+/-15, 95+/-15, AND 100+/-10 REMARK 3 RANGE WITH A FORCE CONSTANT OF 20 KCAL MOL-1 DEG-2 IN THE 50 REMARK 3 ANGLE RANGES BELOW AND ABOVE THESE LIMITS. REMARK 4 REMARK 4 1I0Y COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-FEB-2001. REMARK 100 THE RCSB ID CODE IS RCSB012769. 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 REMARK 210 (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 : ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : NULL REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ARG A 87 GLY A 88 145.17 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1I0W RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF OXIDIZED PARAMAGNETIC CU(II) REMARK 900 PLASTOCYANIN FROM SYNECHOCYSTIS PCC6803 DBREF 1I0Y A 1 98 UNP P21697 PLAS_SYNY3 29 126 SEQADV 1I0Y ASP A 98 UNP P21697 GLU 126 ENGINEERED 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 LYS A 6 0 SHEET 2 A 3 GLU A 28 VAL A 32 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 5 THR A 20 ILE A 23 0 SHEET 2 B 5 GLY A 93 VAL A 97 1 O LYS A 94 N VAL A 21 SHEET 3 B 5 THR A 78 TYR A 82 -1 N TYR A 79 O VAL A 95 SHEET 4 B 5 HIS A 39 ALA A 44 -1 N VAL A 42 O TYR A 82 SHEET 5 B 5 HIS A 58 ALA A 62 -1 O HIS A 58 N ILE A 41 CISPEP 1 GLU A 17 PRO A 18 0 -15.84 CISPEP 2 SER A 37 PRO A 38 0 -8.94 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