HEADER ELECTRON TRANSPORT 16-MAR-96 2CBP TITLE CUCUMBER BASIC PROTEIN, A BLUE COPPER PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CUCUMBER BASIC PROTEIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CUCUMIS SATIVUS; SOURCE 3 ORGANISM_COMMON: CUCUMBER; SOURCE 4 ORGANISM_TAXID: 3659; SOURCE 5 OTHER_DETAILS: FROM SEEDLINGS KEYWDS ELECTRON TRANSPORT, PHYTOCYANIN, TYPE 1 COPPER PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.M.GUSS,H.C.FREEMAN REVDAT 2 24-FEB-09 2CBP 1 VERSN REVDAT 1 21-APR-97 2CBP 0 SPRSDE 21-APR-97 2CBP 1CBP JRNL AUTH J.M.GUSS,E.A.MERRITT,R.P.PHIZACKERLEY,H.C.FREEMAN JRNL TITL THE STRUCTURE OF A PHYTOCYANIN, THE BASIC BLUE JRNL TITL 2 PROTEIN FROM CUCUMBER, REFINED AT 1.8 A RESOLUTION. JRNL REF J.MOL.BIOL. V. 262 686 1996 JRNL REFN ISSN 0022-2836 JRNL PMID 8876647 JRNL DOI 10.1006/JMBI.1996.0545 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.M.GUSS,E.A.MERRITT,R.P.PHIZACKERLEY,B.HEDMAN, REMARK 1 AUTH 2 M.MURATA,K.O.HODGSON,H.C.FREEMAN REMARK 1 TITL PHASE DETERMINATION BY MULTIPLE-WAVELENGTH X-RAY REMARK 1 TITL 2 DIFFRACTION. CRYSTAL STRUCTURE OF A BASIC 'BLUE' REMARK 1 TITL 3 COPPER PROTEIN FROM CUCUMBERS REMARK 1 REF SCIENCE V. 241 806 1988 REMARK 1 REFN ISSN 0036-8075 REMARK 1 REFERENCE 2 REMARK 1 AUTH P.M.COLMAN,H.C.FREEMAN,J.M.GUSS,M.MURATA, REMARK 1 AUTH 2 V.A.NORRIS,J.A.RAMSHAW,M.P.VENKATAPPA,L.E.VICKERY REMARK 1 TITL PRELIMINARY CRYSTALLOGRAPHIC DATA FOR A BASIC REMARK 1 TITL 2 COPPER-CONTAINING PROTEIN FROM CUCUMBER SEEDLINGS REMARK 1 REF J.MOL.BIOL. V. 112 649 1977 REMARK 1 REFN ISSN 0022-2836 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) : 7.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.500 REMARK 3 COMPLETENESS FOR RANGE (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 8124 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.141 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 : 1558 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 122 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.90 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) : 0.15 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) : 0.013 ; 0.030 REMARK 3 ANGLE DISTANCE (A) : 0.027 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.028 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.008 ; 0.020 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.123 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.144 ; 0.500 REMARK 3 MULTIPLE TORSION (A) : 0.199 ; 0.500 REMARK 3 H-BOND (X...Y) (A) : 0.181 ; 0.500 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) : 1.900 ; 5.000 REMARK 3 STAGGERED (DEGREES) : 16.000; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 14.900; 22.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.800 ; 6.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.600 ; 9.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.500 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.400 ; 9.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1988 ESTIMATED COORD. ERROR 0.12 REMARK 3 ANGSTROMS (BACKBONE) ESTIMATED COORD. ERROR 0.17 ANGSTROMS REMARK 3 (SIDE CHAIN) REMARK 4 REMARK 4 2CBP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 1986 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL1-5 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2359, 1.3771, 1.3790, 1.5416 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : AREA DETECTOR REMARK 200 DETECTOR MANUFACTURER : XUONG-HAMLIN MULTIWIRE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43466 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 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 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 (%): 47.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 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 15.44000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.78500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.20500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.78500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.44000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.20500 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 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 ARG A 25 CD - NE - CZ ANGL. DEV. = 10.9 DEGREES REMARK 500 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 3.7 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 THR A 62 17.28 -143.28 REMARK 500 ARG A 65 64.98 -150.67 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 97 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 39 ND1 REMARK 620 2 CYS A 79 SG 138.1 REMARK 620 3 HIS A 84 ND1 99.3 110.4 REMARK 620 4 MET A 89 SD 83.0 110.6 112.1 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 97 DBREF 2CBP A 1 96 UNP P00303 BABL_CUCSA 1 95 SEQADV 2CBP SER A 37 UNP P00303 INSERTION SEQRES 1 A 96 ALA VAL TYR VAL VAL GLY GLY SER GLY GLY TRP THR PHE SEQRES 2 A 96 ASN THR GLU SER TRP PRO LYS GLY LYS ARG PHE ARG ALA SEQRES 3 A 96 GLY ASP ILE LEU LEU PHE ASN TYR ASN PRO SER MET HIS SEQRES 4 A 96 ASN VAL VAL VAL VAL ASN GLN GLY GLY PHE SER THR CYS SEQRES 5 A 96 ASN THR PRO ALA GLY ALA LYS VAL TYR THR SER GLY ARG SEQRES 6 A 96 ASP GLN ILE LYS LEU PRO LYS GLY GLN SER TYR PHE ILE SEQRES 7 A 96 CYS ASN PHE PRO GLY HIS CYS GLN SER GLY MET LYS ILE SEQRES 8 A 96 ALA VAL ASN ALA LEU HET CU A 97 1 HETNAM CU COPPER (II) ION FORMUL 2 CU CU 2+ FORMUL 3 HOH *122(H2 O) HELIX 1 1 ASN A 45 CYS A 52 1 8 SHEET 1 A 3 ALA A 1 VAL A 5 0 SHEET 2 A 3 ASP A 28 TYR A 34 1 N ILE A 29 O ALA A 1 SHEET 3 A 3 GLY A 64 LEU A 70 -1 N GLY A 64 O TYR A 34 SHEET 1 B 4 LYS A 59 TYR A 61 0 SHEET 2 B 4 VAL A 41 VAL A 44 -1 N VAL A 43 O LYS A 59 SHEET 3 B 4 GLY A 73 CYS A 79 -1 N ILE A 78 O VAL A 42 SHEET 4 B 4 MET A 89 ALA A 95 -1 N ALA A 95 O GLY A 73 SSBOND 1 CYS A 52 CYS A 85 1555 1555 2.02 LINK CU CU A 97 ND1 HIS A 39 1555 1555 1.93 LINK CU CU A 97 SG CYS A 79 1555 1555 2.16 LINK CU CU A 97 ND1 HIS A 84 1555 1555 1.95 LINK CU CU A 97 SD MET A 89 1555 1555 2.61 SITE 1 AC1 4 HIS A 39 CYS A 79 HIS A 84 MET A 89 CRYST1 30.880 46.410 65.570 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 0.032383 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021547 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015251 0.00000