1J5D - Header Asymmetric Unit

HEADER ELECTRON TRANSPORT 02-APR-02 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. 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 KEYWDS 2 TRANSPORT

EXPDTA SOLUTION NMR

AUTHOR I.BERTINI,S.CIURLI,A.DIKIY,C.O.FERNANDEZ,C.LUCHINAT, AUTHOR 2 N.SAFAROV,S.SHUMILIN,A.J.VILA

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, 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 J.AM.CHEM.SOC. V. 123 2405 2001 JRNL REFN ISSN 0002-7863 JRNL PMID 11456890 JRNL DOI 10.1021/JA0033685

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 1J5D 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 RCSB ID CODE IS RCSB001632.

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 : 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 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 CYS A 83 SG REMARK 620 2 HIS A 39 ND1 132.2 REMARK 620 3 HIS A 86 ND1 109.0 95.5 REMARK 620 4 MET A 91 SD 109.9 115.6 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) REMARK 900 PLASTOCYANIN FROM SYNECHOCYSTIS PCC6803

DBREF 1J5D A 1 98 UNP P21697 PLAS_SYNY3 29 126

SEQADV 1J5D 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

LINK CU CU A 99 SG CYS A 83 1555 1555 2.34 LINK CU CU A 99 ND1 HIS A 39 1555 1555 2.25 LINK CU CU A 99 ND1 HIS A 86 1555 1555 2.17 LINK CU CU A 99 SD MET A 91 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