HEADER ELECTRON TRANSPORT 24-JUN-02 1M2I TITLE CRYSTAL STRUCTURE OF E44A/E56A MUTANT OF CYTOCHROME B5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME B5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TRYPSIN-SOLUBILIZED FRAGMENT OF CYTOCHROME B5; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 ORGAN: LIVER; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BACTERIA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PUC19 KEYWDS CYTOCHROME B5, TRYPSIN-CLEAVED FRAGMENT, MUTANT;E44A/E56A, ELECTRON KEYWDS 2 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR J.WU,Y.-H.WANG,J.-H.GAN,W.-H.WANG,B.-Y.SUN,Z.-X.HUANG,Z.-X.XIA REVDAT 4 25-OCT-23 1M2I 1 REMARK REVDAT 3 10-NOV-21 1M2I 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1M2I 1 VERSN REVDAT 1 18-MAR-03 1M2I 0 JRNL AUTH J.WU,Y.-H.WANG,J.-H.GAN,W.-H.WANG,B.-Y.SUN,Z.-X.HUANG, JRNL AUTH 2 Z.-X.XIA JRNL TITL STRUCTURES OF CYTOCHROME B5 MUTATED AT THE CHARGED JRNL TITL 2 SURFACE-RESIDUES AND THEIR INTERACTIONS WITH CYTOCHROME C JRNL REF CHIN.J.CHEM. V. 20 1225 2002 JRNL REFN ISSN 1001-604X REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.9 REMARK 3 NUMBER OF REFLECTIONS : 8616 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 SET) : 0.193 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.600 REMARK 3 FREE R VALUE TEST SET COUNT : 915 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 56.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 485 REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE : 0.3170 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 58 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.041 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 662 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 91 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.63000 REMARK 3 B22 (A**2) : -2.81000 REMARK 3 B33 (A**2) : -3.82000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.15 REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.100 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.400 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.070 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.580 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.990 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.63 REMARK 3 BSOL : 104.9 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1M2I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-JUN-02. REMARK 100 THE DEPOSITION ID IS D_1000016515. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-97; 03-APR-99 REMARK 200 TEMPERATURE (KELVIN) : 293.0; 293.0 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N; N REMARK 200 RADIATION SOURCE : SEALED TUBE; SEALED TUBE REMARK 200 BEAMLINE : NULL; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418; 1.5418 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8616 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 19.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 56.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: 1M20 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PHOSPHATE BUFFER, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 35.34650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.24500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.34650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.24500 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NE2 GLN A 13 O HOH A 336 2.16 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 LEU A 23 CA - CB - CG ANGL. DEV. = 14.3 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 ASN A 16 53.99 -148.45 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 HEM A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 39 NE2 REMARK 620 2 HEM A 201 NA 91.7 REMARK 620 3 HEM A 201 NB 91.1 89.4 REMARK 620 4 HEM A 201 NC 88.5 179.7 90.4 REMARK 620 5 HEM A 201 ND 88.0 90.8 179.1 89.4 REMARK 620 6 HIS A 63 NE2 175.1 92.2 91.9 87.6 89.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EHB RELATED DB: PDB REMARK 900 1EHB CONTAINS RECOMBINANT WILD-TYPE TRYPSIN-SOLUBILIZED FRAGMENT OF REMARK 900 CYTOCHROME B5 REMARK 900 RELATED ID: 1ES1 RELATED DB: PDB REMARK 900 1ES1 CONTAINS V61H MUTANT OF TRYPSIN-SOLUBILIZED FRAGMENT OF REMARK 900 CYTOCHROME B5 REMARK 900 RELATED ID: 1LQX RELATED DB: PDB REMARK 900 1LQX CONTAINS V45E MUTANT TRYPSIN-SOLUBILIZED FRAGMENT OF REMARK 900 CYTOCHROME B5 REMARK 900 RELATED ID: 1LR6 RELATED DB: PDB REMARK 900 1LR6 CONTAINS V45Y MUTANT TRYPSIN-SOLUBILIZED FRAGMENT OF REMARK 900 CYTOCHROME B5 REMARK 900 RELATED ID: 1M20 RELATED DB: PDB REMARK 900 1M20 CANTAINS F35Y MUTANT TRYPSIN-SOLUBILIZED FRAGMENT OF REMARK 900 CYTOCHROME B5 REMARK 900 RELATED ID: 1M2M RELATED DB: PDB REMARK 900 1M2M CONTAINS E44A/E48A/E56A/D60A MUTANT TRYPSIN-SOLUBILIZED REMARK 900 FRAGMENT OF CYTOCHROME B5 DBREF 1M2I A 3 84 UNP P00171 CYB5_BOVIN 7 88 SEQADV 1M2I ALA A 44 UNP P00171 GLU 48 ENGINEERED MUTATION SEQADV 1M2I ALA A 56 UNP P00171 GLU 60 ENGINEERED MUTATION SEQRES 1 A 82 ALA VAL LYS TYR TYR THR LEU GLU GLU ILE GLN LYS HIS SEQRES 2 A 82 ASN ASN SER LYS SER THR TRP LEU ILE LEU HIS TYR LYS SEQRES 3 A 82 VAL TYR ASP LEU THR LYS PHE LEU GLU GLU HIS PRO GLY SEQRES 4 A 82 GLY GLU ALA VAL LEU ARG GLU GLN ALA GLY GLY ASP ALA SEQRES 5 A 82 THR ALA ASN PHE GLU ASP VAL GLY HIS SER THR ASP ALA SEQRES 6 A 82 ARG GLU LEU SER LYS THR PHE ILE ILE GLY GLU LEU HIS SEQRES 7 A 82 PRO ASP ASP ARG HET HEM A 201 43 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETSYN HEM HEME FORMUL 2 HEM C34 H32 FE N4 O4 FORMUL 3 HOH *91(H2 O) HELIX 1 1 THR A 8 HIS A 15 1 8 HELIX 2 2 LEU A 32 HIS A 39 1 8 HELIX 3 3 GLU A 43 ALA A 50 1 8 HELIX 4 4 ALA A 54 VAL A 61 1 8 HELIX 5 5 SER A 64 ILE A 75 1 12 HELIX 6 6 HIS A 80 ARG A 84 5 5 SHEET 1 A 5 LYS A 5 TYR A 7 0 SHEET 2 A 5 PHE A 74 HIS A 80 1 O GLU A 78 N TYR A 7 SHEET 3 A 5 TYR A 27 LEU A 32 -1 N VAL A 29 O GLY A 77 SHEET 4 A 5 THR A 21 LEU A 25 -1 O LEU A 23 N TYR A 30 SHEET 5 A 5 GLY A 51 ALA A 54 1 O GLY A 52 N ILE A 24 LINK NE2 HIS A 39 FE HEM A 201 1555 1555 2.10 LINK NE2 HIS A 63 FE HEM A 201 1555 1555 2.02 SITE 1 AC1 14 LEU A 25 PHE A 35 HIS A 39 GLY A 41 SITE 2 AC1 14 VAL A 45 LEU A 46 GLN A 49 ASN A 57 SITE 3 AC1 14 PHE A 58 HIS A 63 SER A 64 ALA A 67 SITE 4 AC1 14 SER A 71 HOH A 305 CRYST1 70.693 40.490 39.199 90.00 111.43 90.00 C 1 2 1 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 0.014146 0.000000 0.005553 0.00000 SCALE2 0.000000 0.024697 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027406 0.00000