HEADER METAL BINDING PROTEIN 31-MAY-09 3HNL TITLE CRYSTAL STRUCTURE OF THE CU-INDUCED DIMER OF THE ENGINEERED CYT CB562 TITLE 2 VARIANT RIDC-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOLUBLE CYTOCHROME B562; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CYTOCHROME B-562; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: CYBC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ELECTRON TRANSPORT, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.N.SALGADO,R.A.LEWIS,J.BRODIN,F.A.TEZCAN REVDAT 5 06-SEP-23 3HNL 1 REMARK REVDAT 4 13-OCT-21 3HNL 1 REMARK SEQADV LINK REVDAT 3 07-MAR-18 3HNL 1 REMARK REVDAT 2 13-JUL-11 3HNL 1 VERSN REVDAT 1 09-FEB-10 3HNL 0 JRNL AUTH E.N.SALGADO,X.I.AMBROGGIO,J.D.BRODIN,R.A.LEWIS,B.KUHLMAN, JRNL AUTH 2 F.A.TEZCAN JRNL TITL METAL TEMPLATED DESIGN OF PROTEIN INTERFACES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 107 1827 2010 JRNL REFN ISSN 0027-8424 JRNL PMID 20080561 JRNL DOI 10.1073/PNAS.0906852107 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 11999 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) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.270 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.900 REMARK 3 FREE R VALUE TEST SET COUNT : 832 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 779 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.35 REMARK 3 BIN R VALUE (WORKING SET) : 0.2330 REMARK 3 BIN FREE R VALUE SET COUNT : 66 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1638 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 207 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : -0.05000 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): 0.346 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.254 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.178 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.375 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.878 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1772 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2422 ; 1.104 ; 2.093 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 210 ; 4.644 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 82 ;47.337 ;26.585 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 292 ;19.146 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 4 ;10.924 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 248 ; 0.075 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1364 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 956 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1199 ; 0.282 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 155 ; 0.160 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.020 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 40 ; 0.189 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 37 ; 0.217 ; 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): 1089 ; 0.373 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1686 ; 0.676 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 779 ; 1.178 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 732 ; 1.870 ; 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 106 3 REMARK 3 1 B 1 B 106 3 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 424 ; 0.050 ; 0.050 REMARK 3 LOOSE POSITIONAL 1 A (A): 395 ; 0.480 ; 5.000 REMARK 3 TIGHT THERMAL 1 A (A**2): 424 ; 0.060 ; 0.500 REMARK 3 LOOSE THERMAL 1 A (A**2): 395 ; 0.910 ;10.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 106 REMARK 3 ORIGIN FOR THE GROUP (A): 12.3410 -11.1870 21.5780 REMARK 3 T TENSOR REMARK 3 T11: -0.0522 T22: -0.1268 REMARK 3 T33: -0.0217 T12: 0.0204 REMARK 3 T13: -0.0242 T23: 0.0029 REMARK 3 L TENSOR REMARK 3 L11: 1.5443 L22: 1.6245 REMARK 3 L33: 3.3576 L12: 0.2899 REMARK 3 L13: -0.7302 L23: 0.3648 REMARK 3 S TENSOR REMARK 3 S11: -0.0320 S12: -0.0234 S13: -0.0736 REMARK 3 S21: 0.0163 S22: 0.0209 S23: -0.1152 REMARK 3 S31: 0.1204 S32: 0.1809 S33: 0.0110 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 106 REMARK 3 ORIGIN FOR THE GROUP (A): 11.9690 8.2140 18.7610 REMARK 3 T TENSOR REMARK 3 T11: -0.0355 T22: -0.1199 REMARK 3 T33: 0.0142 T12: -0.0217 REMARK 3 T13: 0.0155 T23: -0.0091 REMARK 3 L TENSOR REMARK 3 L11: 1.3888 L22: 1.5399 REMARK 3 L33: 3.1556 L12: 0.0198 REMARK 3 L13: 0.7246 L23: 0.1849 REMARK 3 S TENSOR REMARK 3 S11: -0.0815 S12: -0.0263 S13: 0.0361 REMARK 3 S21: -0.0125 S22: 0.0210 S23: -0.0665 REMARK 3 S31: -0.2475 S32: 0.1390 S33: 0.0605 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 3HNL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053354. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : APEX II CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12016 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 22.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.120 REMARK 200 R MERGE (I) : 0.16800 REMARK 200 R SYM (I) : 0.16800 REMARK 200 FOR THE DATA SET : 6.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : 0.48000 REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2QLA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, 200 MM SODIUM CHLORIDE, REMARK 280 25% PEG 3350, 10.7 MM COPPER SULFATE, PH 7.5, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 40.38250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.38250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 33.08250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.52250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 33.08250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.52250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 40.38250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 33.08250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.52250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 40.38250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 33.08250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 43.52250 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -80.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -167.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 40.38250 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 167 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 128 LIES ON A SPECIAL POSITION. 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 SG CYS B 98 CAB HEM B 150 1.72 REMARK 500 SG CYS B 101 CAC HEM B 150 1.73 REMARK 500 SG CYS A 101 CAC HEM A 150 2.12 REMARK 500 SG CYS A 98 CAB HEM A 150 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 131 O HOH B 131 3555 1.82 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 150 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 7 SD REMARK 620 2 HEM A 150 NA 91.3 REMARK 620 3 HEM A 150 NB 87.9 90.1 REMARK 620 4 HEM A 150 NC 89.7 178.2 88.4 REMARK 620 5 HEM A 150 ND 91.1 92.8 176.9 88.7 REMARK 620 6 HIS A 102 NE2 175.4 90.2 87.8 88.7 93.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU B 107 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 63 NE2 REMARK 620 2 HOH A 202 O 92.5 REMARK 620 3 HIS B 73 NE2 88.4 114.9 REMARK 620 4 HIS B 77 NE2 171.3 96.2 88.3 REMARK 620 5 HOH B 180 O 97.9 100.3 144.0 80.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CU A 107 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 73 NE2 REMARK 620 2 HIS A 77 NE2 86.6 REMARK 620 3 HOH A 226 O 99.6 85.6 REMARK 620 4 HIS B 63 NE2 85.0 171.4 93.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 150 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET B 7 SD REMARK 620 2 HEM B 150 NA 87.8 REMARK 620 3 HEM B 150 NB 84.9 87.6 REMARK 620 4 HEM B 150 NC 89.8 175.8 88.7 REMARK 620 5 HEM B 150 ND 90.7 92.5 175.6 91.0 REMARK 620 6 HIS B 102 NE2 173.4 96.2 90.0 85.9 94.3 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 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU A 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 108 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 109 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU B 107 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QLA RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A 16-HELIX BUNDLE ARCHITECTURE PRODUCED BY THE REMARK 900 ZINC-MEDIATED SELF ASSEMBLY OF FOUR CYTOCHROME CB562 MOLECULES REMARK 900 RELATED ID: 2BC5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF E. COLI CYTOCHROME B562 WITH ENGINEERED C-TYPE REMARK 900 HEME LINKAGES REMARK 900 RELATED ID: 3HNI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE ZN-INDUCED TETRAMER OF THE ENGINEERED CYT REMARK 900 CB562 VARIANT RIDC-1 REMARK 900 RELATED ID: 3HNJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE ZN-INDUCED TETRAMER OF THE ENGINEERED CYT REMARK 900 CB562 VARIANT RIDC-2 REMARK 900 RELATED ID: 3HNK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE DIMERIC ASSEMBLY OF THE CYT CB562 VARIANT REMARK 900 RIDC-1 DBREF 3HNL A 1 106 UNP P0ABE7 C562_ECOLX 23 128 DBREF 3HNL B 1 106 UNP P0ABE7 C562_ECOLX 23 128 SEQADV 3HNL ALA A 34 UNP P0ABE7 ARG 56 ENGINEERED MUTATION SEQADV 3HNL ALA A 38 UNP P0ABE7 LEU 60 ENGINEERED MUTATION SEQADV 3HNL TRP A 41 UNP P0ABE7 GLN 63 ENGINEERED MUTATION SEQADV 3HNL SER A 42 UNP P0ABE7 LYS 64 ENGINEERED MUTATION SEQADV 3HNL HIS A 59 UNP P0ABE7 LYS 81 ENGINEERED MUTATION SEQADV 3HNL TRP A 66 UNP P0ABE7 ASP 88 ENGINEERED MUTATION SEQADV 3HNL ILE A 69 UNP P0ABE7 VAL 91 ENGINEERED MUTATION SEQADV 3HNL HIS A 73 UNP P0ABE7 ASP 95 ENGINEERED MUTATION SEQADV 3HNL HIS A 77 UNP P0ABE7 LYS 99 ENGINEERED MUTATION SEQADV 3HNL CYS A 98 UNP P0ABE7 ARG 120 ENGINEERED MUTATION SEQADV 3HNL CYS A 101 UNP P0ABE7 TYR 123 ENGINEERED MUTATION SEQADV 3HNL ALA B 34 UNP P0ABE7 ARG 56 ENGINEERED MUTATION SEQADV 3HNL ALA B 38 UNP P0ABE7 LEU 60 ENGINEERED MUTATION SEQADV 3HNL TRP B 41 UNP P0ABE7 GLN 63 ENGINEERED MUTATION SEQADV 3HNL SER B 42 UNP P0ABE7 LYS 64 ENGINEERED MUTATION SEQADV 3HNL HIS B 59 UNP P0ABE7 LYS 81 ENGINEERED MUTATION SEQADV 3HNL TRP B 66 UNP P0ABE7 ASP 88 ENGINEERED MUTATION SEQADV 3HNL ILE B 69 UNP P0ABE7 VAL 91 ENGINEERED MUTATION SEQADV 3HNL HIS B 73 UNP P0ABE7 ASP 95 ENGINEERED MUTATION SEQADV 3HNL HIS B 77 UNP P0ABE7 LYS 99 ENGINEERED MUTATION SEQADV 3HNL CYS B 98 UNP P0ABE7 ARG 120 ENGINEERED MUTATION SEQADV 3HNL CYS B 101 UNP P0ABE7 TYR 123 ENGINEERED MUTATION SEQRES 1 A 106 ALA ASP LEU GLU ASP ASN MET GLU THR LEU ASN ASP ASN SEQRES 2 A 106 LEU LYS VAL ILE GLU LYS ALA ASP ASN ALA ALA GLN VAL SEQRES 3 A 106 LYS ASP ALA LEU THR LYS MET ALA ALA ALA ALA ALA ASP SEQRES 4 A 106 ALA TRP SER ALA THR PRO PRO LYS LEU GLU ASP LYS SER SEQRES 5 A 106 PRO ASP SER PRO GLU MET HIS ASP PHE ARG HIS GLY PHE SEQRES 6 A 106 TRP ILE LEU ILE GLY GLN ILE HIS ASP ALA LEU HIS LEU SEQRES 7 A 106 ALA ASN GLU GLY LYS VAL LYS GLU ALA GLN ALA ALA ALA SEQRES 8 A 106 GLU GLN LEU LYS THR THR CYS ASN ALA CYS HIS GLN LYS SEQRES 9 A 106 TYR ARG SEQRES 1 B 106 ALA ASP LEU GLU ASP ASN MET GLU THR LEU ASN ASP ASN SEQRES 2 B 106 LEU LYS VAL ILE GLU LYS ALA ASP ASN ALA ALA GLN VAL SEQRES 3 B 106 LYS ASP ALA LEU THR LYS MET ALA ALA ALA ALA ALA ASP SEQRES 4 B 106 ALA TRP SER ALA THR PRO PRO LYS LEU GLU ASP LYS SER SEQRES 5 B 106 PRO ASP SER PRO GLU MET HIS ASP PHE ARG HIS GLY PHE SEQRES 6 B 106 TRP ILE LEU ILE GLY GLN ILE HIS ASP ALA LEU HIS LEU SEQRES 7 B 106 ALA ASN GLU GLY LYS VAL LYS GLU ALA GLN ALA ALA ALA SEQRES 8 B 106 GLU GLN LEU LYS THR THR CYS ASN ALA CYS HIS GLN LYS SEQRES 9 B 106 TYR ARG HET HEM A 150 43 HET CU A 107 1 HET CL A 108 1 HET CL A 109 1 HET HEM B 150 43 HET CU B 107 1 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM CU COPPER (II) ION HETNAM CL CHLORIDE ION HETSYN HEM HEME FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 CU 2(CU 2+) FORMUL 5 CL 2(CL 1-) FORMUL 9 HOH *207(H2 O) HELIX 1 1 ASP A 2 ALA A 20 1 19 HELIX 2 2 ASN A 22 TRP A 41 1 20 HELIX 3 3 PRO A 45 GLU A 49 5 5 HELIX 4 4 SER A 55 GLU A 81 1 27 HELIX 5 5 LYS A 83 LEU A 94 1 12 HELIX 6 6 LEU A 94 ARG A 106 1 13 HELIX 7 7 ASP B 2 ALA B 20 1 19 HELIX 8 8 ASN B 22 TRP B 41 1 20 HELIX 9 9 PRO B 45 GLU B 49 5 5 HELIX 10 10 SER B 55 GLU B 81 1 27 HELIX 11 11 LYS B 83 LEU B 94 1 12 HELIX 12 12 LEU B 94 ARG B 106 1 13 LINK SD MET A 7 FE HEM A 150 1555 1555 2.46 LINK NE2 HIS A 63 CU CU B 107 1555 1555 2.01 LINK NE2 HIS A 73 CU CU A 107 1555 1555 2.17 LINK NE2 HIS A 77 CU CU A 107 1555 1555 2.21 LINK NE2 HIS A 102 FE HEM A 150 1555 1555 2.06 LINK CU CU A 107 O HOH A 226 1555 1555 2.36 LINK CU CU A 107 NE2 HIS B 63 1555 1555 2.11 LINK O HOH A 202 CU CU B 107 1555 1555 2.34 LINK SD MET B 7 FE HEM B 150 1555 1555 2.36 LINK NE2 HIS B 73 CU CU B 107 1555 1555 2.21 LINK NE2 HIS B 77 CU CU B 107 1555 1555 2.21 LINK NE2 HIS B 102 FE HEM B 150 1555 1555 1.98 LINK CU CU B 107 O HOH B 180 1555 1555 2.23 SITE 1 AC1 19 LEU A 3 MET A 7 GLU A 8 LEU A 10 SITE 2 AC1 19 ASN A 11 MET A 33 PRO A 45 PHE A 61 SITE 3 AC1 19 GLY A 64 PHE A 65 CYS A 98 CYS A 101 SITE 4 AC1 19 HIS A 102 ARG A 106 HOH A 117 HOH A 199 SITE 5 AC1 19 ARG B 106 HOH B 138 HOH B 161 SITE 1 AC2 5 HIS A 73 HIS A 77 HOH A 226 HIS B 63 SITE 2 AC2 5 GLU B 81 SITE 1 AC3 4 ALA A 23 HOH A 206 VAL B 84 LYS B 85 SITE 1 AC4 3 HOH A 117 HOH A 118 HOH A 203 SITE 1 AC5 18 ARG A 106 HOH A 123 HOH A 125 GLU B 4 SITE 2 AC5 18 MET B 7 LEU B 14 MET B 33 PRO B 45 SITE 3 AC5 18 PRO B 46 PHE B 61 PHE B 65 CYS B 98 SITE 4 AC5 18 CYS B 101 HIS B 102 ARG B 106 HOH B 164 SITE 5 AC5 18 HOH B 178 HOH B 193 SITE 1 AC6 6 HIS A 63 GLU A 81 HOH A 202 HIS B 73 SITE 2 AC6 6 HIS B 77 HOH B 180 CRYST1 66.165 87.045 80.765 90.00 90.00 90.00 C 2 2 21 16 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 0.015114 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011488 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012382 0.00000