PDB Short entry for 5PCY HEADER ELECTRON TRANSPORT PROTEIN(CUPROPROTEIN)02-SEP-86 5PCY TITLE CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR PLASTOCYANIN AT SIX TITLE 2 PH VALUES COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLASTOCYANIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: POPULUS NIGRA; SOURCE 3 ORGANISM_TAXID: 3691 KEYWDS ELECTRON TRANSPORT PROTEIN(CUPROPROTEIN) EXPDTA X-RAY DIFFRACTION AUTHOR J.M.GUSS,H.C.FREEMAN REVDAT 6 06-MAR-24 5PCY 1 REMARK LINK REVDAT 5 29-NOV-17 5PCY 1 HELIX REVDAT 4 24-FEB-09 5PCY 1 VERSN REVDAT 3 15-JAN-91 5PCY 1 COMPND REVDAT 2 16-APR-87 5PCY 1 COMPND AUTHOR REVDAT 1 15-JAN-87 5PCY 0 JRNL AUTH J.M.GUSS,P.R.HARROWELL,M.MURATA,V.A.NORRIS,H.C.FREEMAN JRNL TITL CRYSTAL STRUCTURE ANALYSES OF REDUCED (CUI) POPLAR JRNL TITL 2 PLASTOCYANIN AT SIX PH VALUES. JRNL REF J.MOL.BIOL. V. 192 361 1986 JRNL REFN ISSN 0022-2836 JRNL PMID 3560221 JRNL DOI 10.1016/0022-2836(86)90371-2 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.B.CHURCH,J.M.GUSS,J.J.POTTER,H.C.FREEMAN REMARK 1 TITL THE CRYSTAL STRUCTURE OF MERCURY-SUBSTITUTED POPLAR REMARK 1 TITL 2 PLASTOCYANIN AT 1.9-ANGSTROMS RESOLUTION REMARK 1 REF J.BIOL.CHEM. V. 261 234 1986 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 2 REMARK 1 AUTH T.P.J.GARRETT,D.J.CLINGELEFFER,J.M.GUSS,S.J.ROGERS, REMARK 1 AUTH 2 H.C.FREEMAN REMARK 1 TITL THE CRYSTAL STRUCTURE OF POPLAR APOPLASTOCYANIN AT REMARK 1 TITL 2 1.8-ANGSTROMS RESOLUTION. THE GEOMETRY OF THE COPPER-BINDING REMARK 1 TITL 3 SITE IS CREATED BY THE POLYPEPTIDE REMARK 1 REF J.BIOL.CHEM. V. 259 2822 1984 REMARK 1 REFN ISSN 0021-9258 REMARK 1 REFERENCE 3 REMARK 1 AUTH J.M.GUSS,H.C.FREEMAN REMARK 1 TITL STRUCTURE OF OXIDIZED POPLAR PLASTOCYANIN AT 1.6 ANGSTROMS REMARK 1 TITL 2 RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 169 521 1983 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 4 REMARK 1 AUTH P.M.COLMAN,H.C.FREEMAN,J.M.GUSS,M.MURATA,V.A.NORRIS, REMARK 1 AUTH 2 J.A.M.RAMSHAW,M.P.VENKATAPPA REMARK 1 TITL X-RAY CRYSTAL STRUCTURE ANALYSIS OF PLASTOCYANIN AT 2.7 REMARK 1 TITL 2 ANGSTROMS RESOLUTION REMARK 1 REF NATURE V. 272 319 1978 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PROLSQ REMARK 3 AUTHORS : KONNERT,HENDRICKSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : NULL REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.160 REMARK 3 R VALUE (WORKING SET) : NULL REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 738 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 44 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE SHORT CONTACT BETWEEN CE1 HIS 87 AND O PRO 36 (3.4 REMARK 3 ANGSTROMS AT PH 7.8, 3.3 ANGSTROMS AT PH 7.0) IS REPLACED REMARK 3 BY A WEAK HYDROGEN BOND (3.1 ANGSTROMS) BETWEEN NE2 HIS 87 REMARK 3 AND O PRO 36 AFTER ROTATION OF THE HIS 87 SIDE CHAIN AT REMARK 3 PH 3.8 (SEE *JRNL* REFERENCE ABOVE). REMARK 4 REMARK 4 5PCY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000179754. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 14.79000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.27000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.28000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.27000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.79000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.28000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 56 CB SER A 56 OG -0.080 REMARK 500 REMARK 500 REMARK: NULL 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 HIS A 37 CG - ND1 - CE1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 42 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 42 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES 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 100 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 37 ND1 REMARK 620 2 CYS A 84 SG 136.3 REMARK 620 3 HIS A 87 ND1 99.1 109.8 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 100 DBREF 5PCY A 1 99 UNP P00299 PLAS1_POPNI 70 168 SEQRES 1 A 99 ILE ASP VAL LEU LEU GLY ALA ASP ASP GLY SER LEU ALA SEQRES 2 A 99 PHE VAL PRO SER GLU PHE SER ILE SER PRO GLY GLU LYS SEQRES 3 A 99 ILE VAL PHE LYS ASN ASN ALA GLY PHE PRO HIS ASN ILE SEQRES 4 A 99 VAL PHE ASP GLU ASP SER ILE PRO SER GLY VAL ASP ALA SEQRES 5 A 99 SER LYS ILE SER MET SER GLU GLU ASP LEU LEU ASN ALA SEQRES 6 A 99 LYS GLY GLU THR PHE GLU VAL ALA LEU SER ASN LYS GLY SEQRES 7 A 99 GLU TYR SER PHE TYR CYS SER PRO HIS GLN GLY ALA GLY SEQRES 8 A 99 MET VAL GLY LYS VAL THR VAL ASN HET CU A 100 1 HETNAM CU COPPER (II) ION FORMUL 2 CU CU 2+ FORMUL 3 HOH *44(H2 O) HELIX 1 A ALA A 52 SER A 56 1ONLY TURN OF HELIX IN MOLCULE 5 SHEET 1 I 4 GLY A 10 VAL A 15 0 SHEET 2 I 4 ILE A 1 ALA A 7 -1 N LEU A 4 O VAL A 15 SHEET 3 I 4 GLU A 25 ASN A 32 1 O LYS A 26 N ILE A 1 SHEET 4 I 4 GLY A 67 LEU A 74 -1 O GLU A 68 N ASN A 31 SHEET 1 II 4 SER A 17 ILE A 21 0 SHEET 2 II 4 MET A 92 ASN A 99 1 N LYS A 95 O SER A 17 SHEET 3 II 4 GLY A 78 CYS A 84 -1 N GLY A 78 O VAL A 98 SHEET 4 II 4 PRO A 36 PRO A 47 -1 N VAL A 40 O TYR A 83 LINK ND1 HIS A 37 CU CU A 100 1555 1555 2.13 LINK SG CYS A 84 CU CU A 100 1555 1555 2.17 LINK ND1 HIS A 87 CU CU A 100 1555 1555 2.39 CISPEP 1 VAL A 15 PRO A 16 0 -13.61 CISPEP 2 PHE A 35 PRO A 36 0 2.10 SITE 1 AC1 4 HIS A 37 CYS A 84 HIS A 87 MET A 92 CRYST1 29.580 46.560 58.540 90.00 90.00 90.00 P 21 21 21 4 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 0.033807 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021478 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017082 0.00000