1YLB - Header Asymmetric Unit

HEADER ELECTRON TRANSPORT 19-JAN-05 1YLB

TITLE NMR SOLUTION STRUCTURE OF THE REDUCED SPINACH PLASTOCYANIN

COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLASTOCYANIN, CHLOROPLAST; COMPND 3 CHAIN: B; COMPND 4 FRAGMENT: REDUCED SPINACH PLASTOCYANIN (RESIDUES 70-168)

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SPINACIA OLERACEA; SOURCE 3 ORGANISM_COMMON: SPINACH; SOURCE 4 ORGANISM_TAXID: 3562

KEYWDS PLASTOCYANIN, COPPER(+)-CONTAINING, ELECTRON-TRANSFER, KEYWDS 2 SPINACH, PHOTOSYNTHESIS, BLUE-COPPER PROTEIN, ELECTRON KEYWDS 3 TRANSPORT

EXPDTA SOLUTION NMR

AUTHOR F.MUSIANI,A.DIKIY,A.Y.SEMENOV,S.CIURLI

REVDAT 3 24-FEB-09 1YLB 1 VERSN REVDAT 2 17-MAY-05 1YLB 1 JRNL REVDAT 1 05-APR-05 1YLB 0

JRNL AUTH F.MUSIANI,A.DIKIY,A.Y.SEMENOV,S.CIURLI JRNL TITL STRUCTURE OF THE INTERMOLECULAR COMPLEX BETWEEN JRNL TITL 2 PLASTOCYANIN AND CYTOCHROME F FROM SPINACH. JRNL REF J.BIOL.CHEM. V. 280 18833 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15691836 JRNL DOI 10.1074/JBC.M412760200

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Y.XUE,M.OKVIST,O.HANSSON,S.YOUNG REMARK 1 TITL CRYSTAL STRUCTURE OF SPINACH PLASTOCYANIN AT 1.7A REMARK 1 TITL 2 RESOLUTION REMARK 1 REF PROTEIN SCI. V. 7 2099 1998 REMARK 1 REFN ISSN 0961-8368 REMARK 1 PMID 9792096

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 6.0 REMARK 3 AUTHORS : CASE, D. A., PEARLMAN, D. A., CALDWELL, J. W., REMARK 3 CHEATHAM III, T. E., ROSS, W. S., SIMMERLING, C. REMARK 3 L., DARDEN, T. A., MERZ, K. M., STANTON, R. V., REMARK 3 CHENG, A. L., VINCENT, J. J., CROWLEY, M., TSUI, REMARK 3 V., RADMER, R. J., DUAN, Y., PITERA, J., REMARK 3 MASSOVA, I., SEIBEL, G. L., SINGH, U. C., REMARK 3 WEINER, P. K., AND KOLLMAN, P. A. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS CALCULATED USING REMARK 3 DIPOLAR (NOESY) DERIVED CONSTRAINTS SUPPLEMENTED WITH PHI AND REMARK 3 PSI DIHEDRAL ANGLE CONSTRAINTS AS WELL AS WITH HYDROGEN BOND REMARK 3 CONSTRAINTS. THE MEAN STRUCTURE OF THE DYANA FAMILY WAS REMARK 3 INITIALLY SUBJECTED TO RESTRAINED ENERGY MINIMIZATION IN VACUO REMARK 3 AND SUBSEQUENTLY TO RESTRAINED MOLECULAR DYNAMICS IN EXPLICIT REMARK 3 WATER MEDIUM. FOR FURTHER EXPERIMENTAL DETAILS PLEASE REFER TO REMARK 3 THE PUBLICATION.

REMARK 4 REMARK 4 1YLB COMPLIES WITH FORMAT V. 3.15, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JAN-05. REMARK 100 THE RCSB ID CODE IS RCSB031647.

REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 50 MM SODIUM PHOSPHATE REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1-2 MM WILD TYPE REDUCED REMARK 210 SPINACH PLASTOCYANIN, 50MM REMARK 210 SODIUM PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, 2D TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 1.3, DYANA 1.5, XEASY REMARK 210 1.3 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS + REMARK 210 RESTRAINED ENERGY MINIMIZATION REMARK 210 + RESTRAINED MOLECULAR DYNAMICS 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 : 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PHE B 82 CG - CD1 - CE1 ANGL. DEV. = -7.4 DEGREES 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 ASP B 9 -39.91 69.17 REMARK 500 ASN B 32 -43.25 -138.34 REMARK 500 GLU B 76 115.53 78.28 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 PHE B 14 0.08 SIDE_CHAIN REMARK 500 PHE B 19 0.09 SIDE_CHAIN REMARK 500 TYR B 80 0.13 SIDE_CHAIN REMARK 500 PHE B 82 0.24 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 CU1 B 100 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 87 ND1 REMARK 620 2 CYS B 84 SG 119.2 REMARK 620 3 HIS B 37 ND1 100.7 124.6 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 CU1 B 100

DBREF 1YLB B 1 99 UNP P00289 PLAS_SPIOL 70 168

SEQRES 1 B 99 VAL GLU VAL LEU LEU GLY GLY GLY ASP GLY SER LEU ALA SEQRES 2 B 99 PHE LEU PRO GLY ASP PHE SER VAL ALA SER GLY GLU GLU SEQRES 3 B 99 ILE VAL PHE LYS ASN ASN ALA GLY PHE PRO HIS ASN VAL SEQRES 4 B 99 VAL PHE ASP GLU ASP GLU ILE PRO SER GLY VAL ASP ALA SEQRES 5 B 99 ALA LYS ILE SER MET SER GLU GLU ASP LEU LEU ASN ALA SEQRES 6 B 99 PRO GLY GLU THR TYR LYS VAL THR LEU THR GLU LYS GLY SEQRES 7 B 99 THR TYR LYS PHE TYR CYS SER PRO HIS GLN GLY ALA GLY SEQRES 8 B 99 MET VAL GLY LYS VAL THR VAL ASN

HET CU1 B 100 1

HETNAM CU1 COPPER (I) ION

FORMUL 2 CU1 CU 1+

HELIX 1 1 ASP B 51 ILE B 55 5 5

SHEET 1 A 4 PHE B 14 LEU B 15 0 SHEET 2 A 4 GLU B 2 LEU B 5 -1 N LEU B 4 O LEU B 15 SHEET 3 A 4 GLU B 26 ASN B 31 1 O LYS B 30 N LEU B 5 SHEET 4 A 4 THR B 69 THR B 73 -1 O VAL B 72 N ILE B 27 SHEET 1 B 3 VAL B 40 PHE B 41 0 SHEET 2 B 3 THR B 79 TYR B 83 -1 O TYR B 83 N VAL B 40 SHEET 3 B 3 VAL B 93 THR B 97 -1 O VAL B 96 N TYR B 80

LINK ND1 HIS B 87 CU CU1 B 100 1555 1555 2.09 LINK SG CYS B 84 CU CU1 B 100 1555 1555 2.12 LINK ND1 HIS B 37 CU CU1 B 100 1555 1555 2.07

CISPEP 1 LEU B 15 PRO B 16 0 -3.88 CISPEP 2 PHE B 35 PRO B 36 0 -3.61

SITE 1 AC1 3 HIS B 37 CYS B 84 HIS B 87

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