10 20 30 40 50 60 70 80 3PI2 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER OXYGEN TRANSPORT 05-NOV-10 3PI2
TITLE CRYSTALLOGRAPHIC STRUCTURE OF HBII-OXY FROM LUCINA PECTINATA AT PH 8.0
COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEMOGLOBIN II; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: LUCINA PECTINATA
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHACOIDES PECTINATUS; SOURCE 3 ORGANISM_COMMON: LUCINA PECTINATA; SOURCE 4 ORGANISM_TAXID: 244486
KEYWDS PH BEHAVIOR, OXYGEN CARRIER, OXYGEN TRANSPORT
EXPDTA X-RAY DIFFRACTION
AUTHOR J.A.GAVIRA,C.A.NIEVES-MARRERO,C.R.RUIZ-MARTINEZ,R.A.ESTREMERA- AUTHOR 2 ANDUJAR,J.LOPEZ-GARRIGA,J.M.GARCIA-RUIZ
REVDAT 2 21-DEC-16 3PI2 1 HET HETNAM LINK REMARK REVDAT 1 09-NOV-11 3PI2 0
JRNL AUTH C.A.NIEVES-MARRERO,C.R.RUIZ-MARTINEZ,R.A.ESTREMERA-ANDUJAR, JRNL AUTH 2 J.LOPEZ-GARRIGA,J.M.GARCIA-RUIZ,J.A.GAVIRA JRNL TITL PH-DEPENDENCE CRYSTALLOGRAPHIC STUDIES OF THE OXYGEN CARRIER JRNL TITL 2 HEMOGLOBIN II FROM LUCINA PECTINATA JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.A.NIEVES-MARRERO,C.R.RUIZ-MARTINEZ,R.A.ESTREMERA-ANDUJAR, REMARK 1 AUTH 2 L.A.GONZALEZ-RAMIREZ,J.LOPEZ-GARRIGA,J.A.GAVIRA REMARK 1 TITL TWO-STEP COUNTERDIFFUSION PROTOCOL FOR THE CRYSTALLIZATION REMARK 1 TITL 2 OF HEAMOGLOBIN II FROM LUCINA PECTINATA IN THE PH RANGE 4-9 REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. F66 264 2010 REMARK 1 REFN ISSN 1744-3091
REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 37050 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1864 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2578 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE SET COUNT : 128 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2356 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 93 REMARK 3 SOLVENT ATOMS : 268 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.07000 REMARK 3 B22 (A**2) : 1.07000 REMARK 3 B33 (A**2) : -2.14000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.116 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.682 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2675 ; 0.029 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3665 ; 2.205 ; 2.041 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3 ; 2.044 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 340 ; 5.361 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;40.282 ;25.085 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 451 ;15.178 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;26.198 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 379 ; 0.174 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2065 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1598 ; 1.539 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1 ; 0.180 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2579 ; 2.460 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1077 ; 4.063 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1078 ; 5.490 ; 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 : 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 : 1.20 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 U VALUES : REFINED INDIVIDUALLY
REMARK 4 REMARK 4 3PI2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-NOV-10. REMARK 100 THE RCSB ID CODE IS RCSB062396.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM16 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90750 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37050 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : 0.06900 REMARK 200 R SYM (I) : 0.06900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.9110 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : 0.49100 REMARK 200 R SYM FOR SHELL (I) : 0.49100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.347 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: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM FORMATE, PH 8.0, CAPILLARY REMARK 280 COUNTERDIFFUSION, TEMPERATURE 293.0K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 37.35300 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.35300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 76.32300 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.35300 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.35300 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 76.32300 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.35300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.35300 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 76.32300 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.35300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.35300 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 76.32300 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 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, 3 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: 5190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 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: 11660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -126.0 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 27300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -245.0 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 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000
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 B 317 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 395 LIES ON A SPECIAL POSITION.
REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 35 CE NZ REMARK 470 ARG A 103 NE CZ NH1 NH2 REMARK 470 LYS A 141 CD CE NZ REMARK 470 LYS A 148 CD CE NZ REMARK 470 GLU A 149 CD OE1 OE2 REMARK 470 SER A 151 OG REMARK 470 ARG B 103 NE CZ NH1 NH2 REMARK 470 LYS B 141 CD CE NZ REMARK 470 LYS B 148 CE NZ REMARK 470 GLU B 149 CG CD OE1 OE2 REMARK 470 SER B 151 OG
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 O HOH A 623 O HOH B 302 2.16 REMARK 500 OD1 ASN A 99 O HOH A 708 2.16 REMARK 500 O HOH A 621 O HOH B 302 2.17 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 ARG A 12 NE - CZ - NH1 ANGL. DEV. = 7.7 DEGREES REMARK 500 ARG A 12 NE - CZ - NH2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ASP A 81 CB - CG - OD1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 81 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ARG B 12 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG B 100 NE - CZ - NH2 ANGL. DEV. = -4.6 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 B 2 15.14 58.75 REMARK 500 ASN B 122 30.36 70.20 REMARK 500 VAL B 125 170.84 -58.67 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 HEM A 500 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 OXY A 501 O2 REMARK 620 2 HEM A 500 NA 88.1 REMARK 620 3 HEM A 500 NB 89.3 95.1 REMARK 620 4 HEM A 500 NC 91.6 177.7 82.6 REMARK 620 5 HEM A 500 ND 92.0 83.2 177.8 99.1 REMARK 620 6 HIS A 97 NE2 174.4 86.4 91.7 94.0 86.9 REMARK 620 7 OXY A 501 O1 25.1 105.6 70.3 73.3 111.4 158.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 OXY B 202 O2 REMARK 620 2 HEM B 201 NA 90.1 REMARK 620 3 HEM B 201 NB 90.5 94.7 REMARK 620 4 HEM B 201 NC 90.7 179.0 84.7 REMARK 620 5 HEM B 201 ND 90.3 84.3 178.6 96.4 REMARK 620 6 HIS B 97 NE2 177.1 87.1 88.7 92.1 90.3 REMARK 620 7 OXY B 202 O1 25.5 107.7 71.2 72.8 110.0 155.6 REMARK 620 N 1 2 3 4 5 6
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 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXY A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HEM B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OXY B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FMT B 203
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2OLP RELATED DB: PDB REMARK 900 RELATED ID: 3PI1 RELATED DB: PDB REMARK 900 RELATED ID: 3PI2 RELATED DB: PDB REMARK 900 RELATED ID: 3PI4 RELATED DB: PDB
DBREF 3PI2 A 1 151 UNP Q86G74 Q86G74_LUCPE 2 152 DBREF 3PI2 B 1 151 UNP Q86G74 Q86G74_LUCPE 2 152
SEQADV 3PI2 ACE A 0 UNP Q86G74 ACETYLATION SEQADV 3PI2 ACE B 0 UNP Q86G74 ACETYLATION
SEQRES 1 A 152 ACE THR THR LEU THR ASN PRO GLN LYS ALA ALA ILE ARG SEQRES 2 A 152 SER SER TRP SER LYS PHE MET ASP ASN GLY VAL SER ASN SEQRES 3 A 152 GLY GLN GLY PHE TYR MET ASP LEU PHE LYS ALA HIS PRO SEQRES 4 A 152 GLU THR LEU THR PRO PHE LYS SER LEU PHE GLY GLY LEU SEQRES 5 A 152 THR LEU ALA GLN LEU GLN ASP ASN PRO LYS MET LYS ALA SEQRES 6 A 152 GLN SER LEU VAL PHE CYS ASN GLY MET SER SER PHE VAL SEQRES 7 A 152 ASP HIS LEU ASP ASP ASN ASP MET LEU VAL VAL LEU ILE SEQRES 8 A 152 GLN LYS MET ALA LYS LEU HIS ASN ASN ARG GLY ILE ARG SEQRES 9 A 152 ALA SER ASP LEU ARG THR ALA TYR ASP ILE LEU ILE HIS SEQRES 10 A 152 TYR MET GLU ASP HIS ASN HIS MET VAL GLY GLY ALA LYS SEQRES 11 A 152 ASP ALA TRP GLU VAL PHE VAL GLY PHE ILE CYS LYS THR SEQRES 12 A 152 LEU GLY ASP TYR MET LYS GLU LEU SER SEQRES 1 B 152 ACE THR THR LEU THR ASN PRO GLN LYS ALA ALA ILE ARG SEQRES 2 B 152 SER SER TRP SER LYS PHE MET ASP ASN GLY VAL SER ASN SEQRES 3 B 152 GLY GLN GLY PHE TYR MET ASP LEU PHE LYS ALA HIS PRO SEQRES 4 B 152 GLU THR LEU THR PRO PHE LYS SER LEU PHE GLY GLY LEU SEQRES 5 B 152 THR LEU ALA GLN LEU GLN ASP ASN PRO LYS MET LYS ALA SEQRES 6 B 152 GLN SER LEU VAL PHE CYS ASN GLY MET SER SER PHE VAL SEQRES 7 B 152 ASP HIS LEU ASP ASP ASN ASP MET LEU VAL VAL LEU ILE SEQRES 8 B 152 GLN LYS MET ALA LYS LEU HIS ASN ASN ARG GLY ILE ARG SEQRES 9 B 152 ALA SER ASP LEU ARG THR ALA TYR ASP ILE LEU ILE HIS SEQRES 10 B 152 TYR MET GLU ASP HIS ASN HIS MET VAL GLY GLY ALA LYS SEQRES 11 B 152 ASP ALA TRP GLU VAL PHE VAL GLY PHE ILE CYS LYS THR SEQRES 12 B 152 LEU GLY ASP TYR MET LYS GLU LEU SER
HET ACE A 0 3 HET ACE B 0 3 HET HEM A 500 43 HET OXY A 501 2 HET HEM B 201 43 HET OXY B 202 2 HET FMT B 203 3
HETNAM ACE ACETYL GROUP HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM OXY OXYGEN MOLECULE HETNAM FMT FORMIC ACID
HETSYN HEM HEME
FORMUL 1 ACE 2(C2 H4 O) FORMUL 3 HEM 2(C34 H32 FE N4 O4) FORMUL 4 OXY 2(O2) FORMUL 7 FMT C H2 O2 FORMUL 8 HOH *268(H2 O)
HELIX 1 1 THR A 4 ASN A 21 1 18 HELIX 2 2 ASN A 21 HIS A 37 1 17 HELIX 3 3 PRO A 38 PRO A 43 5 6 HELIX 4 4 PHE A 44 GLY A 49 1 6 HELIX 5 5 THR A 52 GLN A 57 1 6 HELIX 6 6 ASN A 59 ASP A 78 1 20 HELIX 7 7 ASP A 82 ASN A 99 1 18 HELIX 8 8 ARG A 103 HIS A 121 1 19 HELIX 9 9 GLY A 127 GLU A 149 1 23 HELIX 10 10 THR B 4 ASP B 20 1 17 HELIX 11 11 ASN B 21 HIS B 37 1 17 HELIX 12 12 PRO B 38 PRO B 43 5 6 HELIX 13 13 PHE B 44 GLY B 49 1 6 HELIX 14 14 THR B 52 LEU B 56 5 5 HELIX 15 15 ASN B 59 ASP B 78 1 20 HELIX 16 16 ASP B 82 ASN B 99 1 18 HELIX 17 17 ARG B 103 HIS B 121 1 19 HELIX 18 18 GLY B 127 GLU B 149 1 23
LINK FE HEM A 500 O2 OXY A 501 1555 1555 1.82 LINK FE HEM B 201 O2 OXY B 202 1555 1555 1.86 LINK NE2 HIS B 97 FE HEM B 201 1555 1555 2.14 LINK NE2 HIS A 97 FE HEM A 500 1555 1555 2.19 LINK FE HEM A 500 O1 OXY A 501 1555 1555 2.57 LINK FE HEM B 201 O1 OXY B 202 1555 1555 2.64 LINK N THR B 1 C ACE B 0 1555 1555 1.32 LINK C ACE A 0 N THR A 1 1555 1555 1.33
SITE 1 AC1 23 PRO A 43 PHE A 44 LEU A 47 GLN A 65 SITE 2 AC1 23 VAL A 68 PHE A 69 MET A 73 MET A 93 SITE 3 AC1 23 LEU A 96 HIS A 97 ARG A 100 ILE A 102 SITE 4 AC1 23 ASP A 106 LEU A 107 TYR A 111 OXY A 501 SITE 5 AC1 23 HOH A 607 HOH A 615 HOH A 617 HOH A 652 SITE 6 AC1 23 HOH A 681 LYS B 92 LEU B 96 SITE 1 AC2 4 TYR A 30 PHE A 44 GLN A 65 HEM A 500 SITE 1 AC3 23 LYS A 92 LEU A 96 PRO B 43 PHE B 44 SITE 2 AC3 23 LEU B 47 GLN B 65 VAL B 68 PHE B 69 SITE 3 AC3 23 MET B 73 MET B 93 LEU B 96 HIS B 97 SITE 4 AC3 23 ARG B 100 ILE B 102 LEU B 107 TYR B 111 SITE 5 AC3 23 OXY B 202 HOH B 307 HOH B 314 HOH B 326 SITE 6 AC3 23 HOH B 332 HOH B 379 HOH B 426 SITE 1 AC4 4 TYR B 30 PHE B 44 GLN B 65 HEM B 201 SITE 1 AC5 2 GLU B 39 ASP B 106
CRYST1 74.706 74.706 152.646 90.00 90.00 90.00 P 42 21 2 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 0.013386 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013386 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006551 0.00000