PDB Short entry for 3BQV HEADER ELECTRON TRANSPORT 20-DEC-07 3BQV TITLE CRYSTAL STRUCTURE OF THE DOUBLE MUTANT D44A D45A PLASTOCYANIN FROM TITLE 2 PHORMIDIUM LAMINOSUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLASTOCYANIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 35-139; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHORMIDIUM LAMINOSUM; SOURCE 3 ORGANISM_TAXID: 32059; SOURCE 4 GENE: PETE; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETPCD44/5A KEYWDS PLASTOCYANIN, ELECTRON TRANSPORT, PHOTOSYSTEM 1, COPPER, METAL- KEYWDS 2 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR R.FROMME,Y.S.BUKHMAN-DERUYTER,H.MI,P.FROMME REVDAT 4 30-AUG-23 3BQV 1 REMARK REVDAT 3 20-OCT-21 3BQV 1 REMARK SEQADV REVDAT 2 25-OCT-17 3BQV 1 REMARK REVDAT 1 06-JAN-09 3BQV 0 JRNL AUTH Y.S.BUKHMAN-DERUYTER,R.FROMME,I.GROTJOHANN,B.SCHLARB-RIDLEY, JRNL AUTH 2 H.MI,P.FROMME JRNL TITL HIGH RESOLUTION STRUCTURES OF PLASTOCYANIN FROM PHORMIDIUM JRNL TITL 2 LAMINOSUM AND D44A, D45A DOUBLE MUTANT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 13102 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 704 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 928 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE SET COUNT : 64 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 799 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.92 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.38000 REMARK 3 B22 (A**2) : -0.15000 REMARK 3 B33 (A**2) : -0.23000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.133 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.103 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.061 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.569 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 828 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1128 ; 1.348 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 106 ; 5.695 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 33 ;25.716 ;24.848 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 128 ;11.280 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 1 ; 2.648 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 123 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 637 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 381 ; 0.217 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 546 ; 0.314 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 124 ; 0.123 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 28 ; 0.125 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 25 ; 0.098 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 540 ; 1.081 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 850 ; 1.605 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 328 ; 2.224 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 277 ; 3.054 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 868 ; 1.617 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 155 ; 2.539 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 804 ; 1.934 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3BQV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JAN-08. REMARK 100 THE DEPOSITION ID IS D_1000045854. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-DEC-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13923 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.9600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.63000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2Q5B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 8000, 0.1 M SODIUM CACODYLATE, REMARK 280 0.2 M SODIUM ACETATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K 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 16.66100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.01300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.88900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.01300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.66100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 16.88900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 106 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Q5B RELATED DB: PDB REMARK 900 HIGH RESOLUTION WILD TYPE FROM PHORMIDIUM LAMINOSUM REMARK 900 RELATED ID: 1BAW RELATED DB: PDB REMARK 900 MEDIUM RESOLUTION WILD TYPE FROM PHORMIDIUM LAMINOSUM REMARK 900 RELATED ID: 1PLC RELATED DB: PDB REMARK 900 1.33 A RESOLUTION STRUCTURE FROM POPLAR REMARK 900 RELATED ID: 1BXV RELATED DB: PDB REMARK 900 REDUCED PLASTOCYANIN FROM SYNECHOCOCCUS SP. (1.8A) REMARK 900 RELATED ID: 1BYP RELATED DB: PDB REMARK 900 E43K D44K DOUBLE MUTANT FROM PLASTOCYANIN FROM SILENE REMARK 900 RELATED ID: 1IUZ RELATED DB: PDB REMARK 900 ULVA PERTUSA PLASTOCYANIN AT 1.6-A REMARK 900 RELATED ID: 1PCS RELATED DB: PDB REMARK 900 TRIPLE MUTANT PLASTOCYANIN FROM THE CYANOBACTERIUM SYNECHOCYSTIS REMARK 900 SP. PCC6803 DBREF 3BQV A 1 105 UNP Q51883 PLAS_PHOLA 35 139 SEQADV 3BQV ALA A 44 UNP Q51883 ASP 78 ENGINEERED MUTATION SEQADV 3BQV ALA A 45 UNP Q51883 ASP 79 ENGINEERED MUTATION SEQRES 1 A 105 GLU THR PHE THR VAL LYS MET GLY ALA ASP SER GLY LEU SEQRES 2 A 105 LEU GLN PHE GLU PRO ALA ASN VAL THR VAL HIS PRO GLY SEQRES 3 A 105 ASP THR VAL LYS TRP VAL ASN ASN LYS LEU PRO PRO HIS SEQRES 4 A 105 ASN ILE LEU PHE ALA ALA LYS GLN VAL PRO GLY ALA SER SEQRES 5 A 105 LYS GLU LEU ALA ASP LYS LEU SER HIS SER GLN LEU MET SEQRES 6 A 105 PHE SER PRO GLY GLU SER TYR GLU ILE THR PHE SER SER SEQRES 7 A 105 ASP PHE PRO ALA GLY THR TYR THR TYR TYR CYS ALA PRO SEQRES 8 A 105 HIS ARG GLY ALA GLY MET VAL GLY LYS ILE THR VAL GLU SEQRES 9 A 105 GLY HET CU A 106 1 HETNAM CU COPPER (II) ION FORMUL 2 CU CU 2+ FORMUL 3 HOH *154(H2 O) HELIX 1 1 ALA A 45 ALA A 51 5 7 HELIX 2 2 SER A 52 SER A 60 1 9 SHEET 1 A 4 PHE A 16 GLU A 17 0 SHEET 2 A 4 THR A 2 MET A 7 -1 N LYS A 6 O GLU A 17 SHEET 3 A 4 THR A 28 ASN A 33 1 O THR A 28 N PHE A 3 SHEET 4 A 4 SER A 71 THR A 75 -1 O TYR A 72 N TRP A 31 SHEET 1 B 5 ASN A 20 VAL A 23 0 SHEET 2 B 5 VAL A 98 VAL A 103 1 O THR A 102 N VAL A 23 SHEET 3 B 5 GLY A 83 TYR A 88 -1 N GLY A 83 O VAL A 103 SHEET 4 B 5 HIS A 39 PHE A 43 -1 N LEU A 42 O TYR A 88 SHEET 5 B 5 HIS A 61 MET A 65 -1 O HIS A 61 N ILE A 41 LINK ND1 HIS A 39 CU CU A 106 1555 1555 2.04 CISPEP 1 GLU A 17 PRO A 18 0 -3.13 CISPEP 2 PRO A 37 PRO A 38 0 3.71 SITE 1 AC1 4 HIS A 39 CYS A 89 HIS A 92 MET A 97 CRYST1 33.322 33.778 78.026 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 0.030010 0.000000 0.000000 0.00000 SCALE2 0.000000 0.029605 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012816 0.00000