HEADER ELECTRON TRANSPORT 02-APR-02 1J5D TITLE SOLUTION STRUCTURE OF OXIDIZED PARAMAGNETIC CU(II) PLASTOCYANIN FROM TITLE 2 SYNECHOCYSTIS PCC6803-MINIMIZED AVERAGE 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. 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 AUTHOR I.BERTINI,S.CIURLI,A.DIKIY,C.O.FERNANDEZ,C.LUCHINAT,N.SAFAROV, AUTHOR 2 S.SHUMILIN,A.J.VILA REVDAT 4 27-DEC-23 1J5D 1 REMARK REVDAT 3 27-OCT-21 1J5D 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1J5D 1 VERSN REVDAT 1 10-APR-02 1J5D 0 SPRSDE 10-APR-02 1J5D 1I0Y 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, AMBER 5.0 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUENTERT (DYANA), KOLLMAN REMARK 3 (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 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. THE MEAN STRUCTURE FROM THE DYANA FAMILY WAS REMARK 3 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 WITH REMARK 3 A CUT-OFF OF 10 A. THE MIXED LINEAR-HARMONIC FLAT-BOTTOMED REMARK 3 POTENTIAL IMPLEMENTED IN SANDER WAS APPLIED TO ALL STRUCTURAL REMARK 3 CONSTRAINTS. THIS POTENTIAL INVOLVES A NULL FORCE CONSTANT FOR REMARK 3 STRUCTURAL CONSTRAINTS WITHIN THE ALLOWED LIMITS, A NON-ZERO REMARK 3 HARMONIC FORCE CONSTANT IN A SMALL INTERVAL OUTSIDE THE ALLOWED REMARK 3 LIMITS, AND A LINEARLY DEPENDENT POTENTIAL BEYOND THAT LIMIT. REMARK 3 NOE-DERIVED DISTANCE CONSTRAINTS WERE RESTRICTED BELOW THE UPPER REMARK 3 DISTANCE LIMIT (RI), USING A FORCE CONSTANT OF 32 KCAL MOL-1 A-2 REMARK 3 FOR THE INTERVAL RI+0.5 A. DISTANCE CONSTRAINTS INVOLVING THE REMARK 3 SAME H-BONDS USED FOR DYANA CALCULATIONS WERE INCLUDED IN THE REMARK 3 REM CALCULATION, RESTRICTING THE NH...O AND N...O DISTANCES TO REMARK 3 THE SAME UPPER (RI) VALUES USED IN DYANA, WITH A FORCE CONSTANT REMARK 3 OF 32 KCAL MOL-1 A-2 FOR THE RANGE RI + 0.5 A. THE CU-H REMARK 3 DISTANCES DERIVED FROM THE ANALYSIS OF THE NON-SELECTIVE REMARK 3 LONGITUDINAL RELAXATION RATES WERE ALSO RESTRAINED TO THE SAME REMARK 3 UPPER (RI) LIMITS USED IN DYANA, WITH A FORCE CONSTANT OF 32 REMARK 3 KCAL MOL-1 A-2 FOR RI + 0.5 A. THE CU-NHIS AND CU-SCYS DISTANCES REMARK 3 WERE CONSTRAINED AT 2.1+/-0.1 A AND 2.2+/-0.1 A, RESPECTIVELY, REMARK 3 USING A LINEAR-HARMONIC FLAT-BOTTOMED POTENTIAL WITH FORCE REMARK 3 CONSTANTS OF 50 KCAL MOL-1 A-2 IN THE 0.3-A DISTANCE RANGES REMARK 3 BELOW AND ABOVE THESE LIMITS. THE CU-SMET DISTANCE WAS REMARK 3 ANALOGOUSLY CONSTRAINED WITHIN THE 2.75+/-0.05 A RANGE, USING A REMARK 3 FORCE CONSTANT OF 40 KCAL MOL-1 A-2. THE CU-N(HIS)-CG, CU-N(HIS)- REMARK 3 CE, CU-S(CYS)-CB, CU-S(MET)-CG, AND CU-S(MET)-CE ANGLES WERE REMARK 3 RESTRAINED AROUND 127+/-0, 127+/-0, 105+/-5, 130+/-10, 110+/-10, REMARK 3 RESPECTIVELY, USING A LINEAR-HARMONIC FLAT-BOTTOMED POTENTIAL REMARK 3 WITH FORCE CONSTANTS OF 50 KCAL MOL-1 DEG-2 IN THE 50 RANGES REMARK 3 BELOW AND ABOVE THE GIVEN VALUES. ANALOGOUSLY, THE (HIS)N-CU- REMARK 3 N(HIS), (HIS)N-CU-S(CYS), (HIS)N-CU-S(MET), AND (MET)S-CU-S(CYS) REMARK 3 ANGLES WERE RESTRAINED IN THE 110+/-10, 125+/-15, 95+/-15, AND REMARK 3 100+/-10 RANGE WITH A FORCE CONSTANT OF 20 KCAL MOL-1 DEG-2 IN REMARK 3 THE 50 ANGLE RANGES BELOW AND ABOVE THESE LIMITS. REMARK 4 REMARK 4 1J5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-02. REMARK 100 THE DEPOSITION ID IS D_1000001632. 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 : ENERGY MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 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 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: 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 ALA A 25 102.41 -56.57 REMARK 500 ASN A 34 -74.16 -79.50 REMARK 500 GLU A 84 -68.26 -23.00 REMARK 500 REMARK 500 REMARK: NULL 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 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 87 0.08 SIDE CHAIN 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 132.2 REMARK 620 3 HIS A 86 ND1 95.5 109.0 REMARK 620 4 MET A 91 SD 115.6 109.9 76.4 REMARK 620 N 1 2 3 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: 1J5C RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF OXIDIZED PARAMAGNETIC CU(II) PLASTOCYANIN REMARK 900 FROM SYNECHOCYSTIS PCC6803 DBREF 1J5D A 1 98 UNP P21697 PLAS_SYNY3 29 126 SEQADV 1J5D 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 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 LINK ND1 HIS A 39 CU CU A 99 1555 1555 2.25 LINK SG CYS A 83 CU CU A 99 1555 1555 2.34 LINK ND1 HIS A 86 CU CU A 99 1555 1555 2.17 LINK SD MET A 91 CU CU A 99 1555 1555 2.66 CISPEP 1 GLU A 17 PRO A 18 0 -15.84 CISPEP 2 SER A 37 PRO A 38 0 -8.94 SITE 1 AC1 4 HIS A 39 CYS A 83 HIS A 86 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