HEADER MEMBRANE PROTEIN 09-SEP-20 7ABW TITLE CRYSTAL STRUCTURE OF SIDEROPHORE REDUCTASE FOXB COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPSY DOMAIN-CONTAINING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PEPTIDASE; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 287; SOURCE 4 GENE: ALP65_03579, CAZ10_13355, DY930_33720, ECC04_000260, SOURCE 5 F7O90_26595, IPC36_29360, IPC669_34100, NCTC12951_00372, SOURCE 6 NCTC13621_01916, PAEAG1_03004, RW109_RW109_03547; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MEMBRANE PROTEIN REDUCTASE SIDEROPHORE, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.JOSTS,H.TIDOW REVDAT 1 01-SEP-21 7ABW 0 JRNL AUTH I.JOSTS,K.VEITH,V.NORMANT,I.J.SCHALK,H.TIDOW JRNL TITL STRUCTURAL INSIGHTS INTO A NOVEL FAMILY OF INTEGRAL MEMBRANE JRNL TITL 2 SIDEROPHORE REDUCTASES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 34417315 JRNL DOI 10.1073/PNAS.2101952118 REMARK 2 REMARK 2 RESOLUTION. 3.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 3.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 59.3 REMARK 3 NUMBER OF REFLECTIONS : 14617 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) : 0.266 REMARK 3 R VALUE (WORKING SET) : 0.265 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 767 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) : 3.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 83 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 4.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE SET COUNT : 4 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5774 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 273 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.83000 REMARK 3 B22 (A**2) : 2.78000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.780 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.422 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 53.980 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.812 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.754 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6263 ; 0.014 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 5731 ; 0.017 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8553 ; 2.001 ; 1.695 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13149 ; 1.811 ; 1.623 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 721 ; 7.522 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 332 ;30.361 ;19.910 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 872 ;14.726 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 52 ;17.795 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 688 ; 0.244 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7041 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1575 ; 0.022 ; 0.020 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 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 505 REMARK 3 ORIGIN FOR THE GROUP (A): 3.8879 24.1083 2.0802 REMARK 3 T TENSOR REMARK 3 T11: 0.2206 T22: 0.0160 REMARK 3 T33: 0.0440 T12: 0.0053 REMARK 3 T13: 0.0353 T23: -0.0183 REMARK 3 L TENSOR REMARK 3 L11: 2.2286 L22: 1.0223 REMARK 3 L33: 0.8048 L12: 0.5359 REMARK 3 L13: 0.7709 L23: 0.3085 REMARK 3 S TENSOR REMARK 3 S11: 0.0219 S12: -0.0913 S13: 0.1969 REMARK 3 S21: -0.0379 S22: -0.0022 S23: -0.0758 REMARK 3 S31: -0.1890 S32: 0.0289 S33: -0.0197 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 504 REMARK 3 ORIGIN FOR THE GROUP (A): 61.8636 24.7377 26.7178 REMARK 3 T TENSOR REMARK 3 T11: 0.2405 T22: 0.1051 REMARK 3 T33: 0.0891 T12: -0.0899 REMARK 3 T13: 0.0339 T23: 0.0312 REMARK 3 L TENSOR REMARK 3 L11: 3.4714 L22: 0.4150 REMARK 3 L33: 1.2271 L12: 0.0015 REMARK 3 L13: -0.6328 L23: 0.1825 REMARK 3 S TENSOR REMARK 3 S11: 0.0590 S12: -0.3974 S13: 0.0605 REMARK 3 S21: 0.0047 S22: 0.0076 S23: 0.0397 REMARK 3 S31: 0.0342 S32: -0.0164 S33: -0.0666 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: U VALUES : WITH TLS ADDED HYDROGENS REMARK 3 HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 7ABW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1292110767. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.987 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15384 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.350 REMARK 200 RESOLUTION RANGE LOW (A) : 47.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 200 DATA REDUNDANCY : 19.30 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.3 REMARK 200 DATA REDUNDANCY IN SHELL : 13.30 REMARK 200 R MERGE FOR SHELL (I) : 1.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: SHELXCD REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG600 100 MM BICINE PH9 100 MM REMARK 280 ZNSO4, VAPOR DIFFUSION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 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 -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 118.53250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.16050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 118.53250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 57.16050 REMARK 290 SMTRY3 4 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: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ARG A 171 REMARK 465 GLY A 172 REMARK 465 ARG A 173 REMARK 465 PRO A 174 REMARK 465 PHE A 175 REMARK 465 TRP A 176 REMARK 465 SER A 177 REMARK 465 LYS A 178 REMARK 465 TRP A 179 REMARK 465 THR A 180 REMARK 465 THR A 181 REMARK 465 ALA A 182 REMARK 465 TRP A 183 REMARK 465 LYS A 184 REMARK 465 ILE A 185 REMARK 465 LYS A 186 REMARK 465 ARG A 187 REMARK 465 GLY A 188 REMARK 465 TRP A 379 REMARK 465 ASN A 380 REMARK 465 GLY A 381 REMARK 465 ARG A 382 REMARK 465 GLY B 172 REMARK 465 ARG B 173 REMARK 465 PRO B 174 REMARK 465 PHE B 175 REMARK 465 TRP B 176 REMARK 465 SER B 177 REMARK 465 LYS B 178 REMARK 465 TRP B 179 REMARK 465 THR B 180 REMARK 465 THR B 181 REMARK 465 ALA B 182 REMARK 465 TRP B 183 REMARK 465 LYS B 184 REMARK 465 ILE B 185 REMARK 465 LYS B 186 REMARK 465 ARG B 187 REMARK 465 GLY B 188 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 HIS B 298 ZN ZN B 406 1.04 REMARK 500 O HIS B 378 O GLY B 381 1.66 REMARK 500 NE2 HIS B 339 NB HEM B 402 2.15 REMARK 500 OG SER B 55 OD1 ASP B 260 2.17 REMARK 500 OG1 THR B 89 O ASP B 101 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 111 CD GLU A 111 OE1 -0.077 REMARK 500 TYR B 336 C PRO B 337 N 0.162 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 20 CB - CG - CD1 ANGL. DEV. = -10.8 DEGREES REMARK 500 GLY A 110 N - CA - C ANGL. DEV. = -30.6 DEGREES REMARK 500 ARG A 333 NE - CZ - NH1 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 372 CD - NE - CZ ANGL. DEV. = 12.2 DEGREES REMARK 500 ARG A 372 NE - CZ - NH1 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 375 CG - CD - NE ANGL. DEV. = 13.9 DEGREES REMARK 500 HIS B 83 CB - CA - C ANGL. DEV. = 28.4 DEGREES REMARK 500 HIS B 83 N - CA - C ANGL. DEV. = -18.6 DEGREES REMARK 500 PRO B 84 C - N - CD ANGL. DEV. = -18.4 DEGREES REMARK 500 ARG B 199 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 PRO B 337 C - N - CA ANGL. DEV. = 12.2 DEGREES REMARK 500 GLY B 381 N - CA - C ANGL. DEV. = -25.2 DEGREES REMARK 500 ARG B 382 C - N - CA ANGL. DEV. = 15.3 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 41 52.01 -144.62 REMARK 500 ALA A 80 -5.59 79.57 REMARK 500 GLU A 93 33.67 -98.90 REMARK 500 ALA A 94 -62.74 68.53 REMARK 500 ASP A 101 -15.82 -143.07 REMARK 500 THR A 140 41.21 39.21 REMARK 500 ASN A 144 -9.02 -59.69 REMARK 500 VAL A 225 -58.61 -120.23 REMARK 500 HIS B 83 154.35 80.34 REMARK 500 GLU B 99 -55.87 71.31 REMARK 500 ALA B 119 -174.40 -175.21 REMARK 500 CYS B 122 -64.63 -97.74 REMARK 500 SER B 326 -157.03 -99.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 372 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PE5 A 403 REMARK 610 DMU A 404 REMARK 610 DMU B 403 REMARK 610 DMU B 404 REMARK 610 DMU B 405 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 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 9 NE2 REMARK 620 2 HEM A 401 NA 84.9 REMARK 620 3 HEM A 401 NB 96.5 89.4 REMARK 620 4 HEM A 401 NC 93.0 173.2 84.4 REMARK 620 5 HEM A 401 ND 78.8 92.3 174.8 93.6 REMARK 620 6 HIS A 198 NE2 176.7 91.8 83.2 90.2 101.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 407 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 34 NE2 REMARK 620 2 HIS A 83 NE2 122.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 402 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 136 NE2 REMARK 620 2 HEM A 402 NA 91.2 REMARK 620 3 HEM A 402 NB 90.0 86.4 REMARK 620 4 HEM A 402 NC 87.6 171.0 84.8 REMARK 620 5 HEM A 402 ND 93.7 95.2 176.0 93.8 REMARK 620 6 HIS A 339 NE2 170.7 92.6 81.7 87.4 94.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 9 NE2 REMARK 620 2 HEM B 401 NA 91.3 REMARK 620 3 HEM B 401 NB 86.1 85.5 REMARK 620 4 HEM B 401 NC 90.3 172.9 87.7 REMARK 620 5 HEM B 401 ND 96.6 93.0 176.9 93.7 REMARK 620 6 HIS B 198 NE2 171.2 92.4 86.2 85.1 91.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 402 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 136 NE2 REMARK 620 2 HEM B 402 NA 92.7 REMARK 620 3 HEM B 402 NB 92.3 87.2 REMARK 620 4 HEM B 402 NC 91.3 172.1 85.8 REMARK 620 5 HEM B 402 ND 94.1 94.5 173.3 92.1 REMARK 620 6 HIS B 339 NE2 147.1 88.9 54.9 84.0 118.6 REMARK 620 N 1 2 3 4 5 DBREF1 7ABW A 1 382 UNP A0A0C7CRS7_PSEAI DBREF2 7ABW A A0A0C7CRS7 1 382 DBREF1 7ABW B 1 382 UNP A0A0C7CRS7_PSEAI DBREF2 7ABW B A0A0C7CRS7 1 382 SEQRES 1 A 382 MET ARG PRO VAL LEU VAL LEU LEU HIS ARG TYR VAL GLY SEQRES 2 A 382 LEU ALA THR ALA LEU PHE LEU PHE LEU ALA GLY LEU THR SEQRES 3 A 382 GLY SER LEU LEU ALA PHE HIS HIS GLU ILE ASP GLU TRP SEQRES 4 A 382 LEU ASN PRO GLY PHE TYR ALA VAL GLY GLU GLY GLY GLU SEQRES 5 A 382 ARG LEU SER PRO GLY SER LEU VAL GLN ARG VAL GLU SER SEQRES 6 A 382 ARG TYR PRO ARG GLN LEU VAL TRP TYR MET GLU TYR PRO SEQRES 7 A 382 GLU ALA GLY GLY HIS PRO ALA LEU LEU ALA THR VAL PRO SEQRES 8 A 382 ARG GLU ALA GLY ALA LYS VAL GLU HIS ASP VAL PHE TYR SEQRES 9 A 382 LEU ASP PRO VAL SER GLY GLU GLU VAL GLY LYS ARG LEU SEQRES 10 A 382 TRP ALA ALA CYS CYS PHE GLN PRO ALA ASN LEU VAL PRO SEQRES 11 A 382 TRP VAL LEU GLU PHE HIS HIS ASN LEU THR LEU PRO GLY SEQRES 12 A 382 ASN TRP GLY LEU TYR LEU MET GLY GLY VAL ALA MET PHE SEQRES 13 A 382 TRP PHE LEU ASP CYS PHE VAL GLY ALA TRP LEU THR LEU SEQRES 14 A 382 PRO ARG GLY ARG PRO PHE TRP SER LYS TRP THR THR ALA SEQRES 15 A 382 TRP LYS ILE LYS ARG GLY ASN ALA TYR ARG PHE ASN PHE SEQRES 16 A 382 ASP LEU HIS ARG ALA GLY GLY LEU TRP LEU TRP LEU LEU SEQRES 17 A 382 LEU ALA PRO VAL ALA LEU SER SER VAL ALA LEU ASN LEU SEQRES 18 A 382 PRO SER GLN VAL PHE LYS PRO LEU VAL SER LEU PHE SER SEQRES 19 A 382 PRO ILE GLU PRO SER VAL TYR GLU ALA ARG GLY ARG LEU SEQRES 20 A 382 PRO ARG GLU GLN LEU GLY GLU THR ARG LEU ASP TYR ASP SEQRES 21 A 382 ARG THR PHE GLN LEU ALA SER VAL GLU ALA ALA ARG LEU SEQRES 22 A 382 GLY ILE ALA GLU PRO ILE GLY GLU LEU TYR TYR SER PHE SEQRES 23 A 382 GLU TYR ASN PHE PHE GLY ALA GLY PHE GLY ASP HIS ASP SEQRES 24 A 382 ASP PRO MET GLY LYS SER TRP LEU PHE PHE HIS GLY SER SEQRES 25 A 382 ASP GLY ARG LEU LEU GLY GLN GLU VAL ALA GLY GLN GLY SEQRES 26 A 382 SER TRP GLY GLU ARG PHE TYR ARG LEU GLN TYR PRO ILE SEQRES 27 A 382 HIS GLY GLY ARG ILE ALA GLY LEU PRO GLY ARG ILE ALA SEQRES 28 A 382 ILE ALA ALA LEU GLY LEU ALA ILE ALA GLY LEU SER LEU SEQRES 29 A 382 THR GLY VAL TYR ILE TRP TRP ARG LYS ARG ARG ALA ARG SEQRES 30 A 382 HIS TRP ASN GLY ARG SEQRES 1 B 382 MET ARG PRO VAL LEU VAL LEU LEU HIS ARG TYR VAL GLY SEQRES 2 B 382 LEU ALA THR ALA LEU PHE LEU PHE LEU ALA GLY LEU THR SEQRES 3 B 382 GLY SER LEU LEU ALA PHE HIS HIS GLU ILE ASP GLU TRP SEQRES 4 B 382 LEU ASN PRO GLY PHE TYR ALA VAL GLY GLU GLY GLY GLU SEQRES 5 B 382 ARG LEU SER PRO GLY SER LEU VAL GLN ARG VAL GLU SER SEQRES 6 B 382 ARG TYR PRO ARG GLN LEU VAL TRP TYR MET GLU TYR PRO SEQRES 7 B 382 GLU ALA GLY GLY HIS PRO ALA LEU LEU ALA THR VAL PRO SEQRES 8 B 382 ARG GLU ALA GLY ALA LYS VAL GLU HIS ASP VAL PHE TYR SEQRES 9 B 382 LEU ASP PRO VAL SER GLY GLU GLU VAL GLY LYS ARG LEU SEQRES 10 B 382 TRP ALA ALA CYS CYS PHE GLN PRO ALA ASN LEU VAL PRO SEQRES 11 B 382 TRP VAL LEU GLU PHE HIS HIS ASN LEU THR LEU PRO GLY SEQRES 12 B 382 ASN TRP GLY LEU TYR LEU MET GLY GLY VAL ALA MET PHE SEQRES 13 B 382 TRP PHE LEU ASP CYS PHE VAL GLY ALA TRP LEU THR LEU SEQRES 14 B 382 PRO ARG GLY ARG PRO PHE TRP SER LYS TRP THR THR ALA SEQRES 15 B 382 TRP LYS ILE LYS ARG GLY ASN ALA TYR ARG PHE ASN PHE SEQRES 16 B 382 ASP LEU HIS ARG ALA GLY GLY LEU TRP LEU TRP LEU LEU SEQRES 17 B 382 LEU ALA PRO VAL ALA LEU SER SER VAL ALA LEU ASN LEU SEQRES 18 B 382 PRO SER GLN VAL PHE LYS PRO LEU VAL SER LEU PHE SER SEQRES 19 B 382 PRO ILE GLU PRO SER VAL TYR GLU ALA ARG GLY ARG LEU SEQRES 20 B 382 PRO ARG GLU GLN LEU GLY GLU THR ARG LEU ASP TYR ASP SEQRES 21 B 382 ARG THR PHE GLN LEU ALA SER VAL GLU ALA ALA ARG LEU SEQRES 22 B 382 GLY ILE ALA GLU PRO ILE GLY GLU LEU TYR TYR SER PHE SEQRES 23 B 382 GLU TYR ASN PHE PHE GLY ALA GLY PHE GLY ASP HIS ASP SEQRES 24 B 382 ASP PRO MET GLY LYS SER TRP LEU PHE PHE HIS GLY SER SEQRES 25 B 382 ASP GLY ARG LEU LEU GLY GLN GLU VAL ALA GLY GLN GLY SEQRES 26 B 382 SER TRP GLY GLU ARG PHE TYR ARG LEU GLN TYR PRO ILE SEQRES 27 B 382 HIS GLY GLY ARG ILE ALA GLY LEU PRO GLY ARG ILE ALA SEQRES 28 B 382 ILE ALA ALA LEU GLY LEU ALA ILE ALA GLY LEU SER LEU SEQRES 29 B 382 THR GLY VAL TYR ILE TRP TRP ARG LYS ARG ARG ALA ARG SEQRES 30 B 382 HIS TRP ASN GLY ARG HET HEM A 401 43 HET HEM A 402 43 HET PE5 A 403 17 HET DMU A 404 12 HET DMU A 405 33 HET ZN A 406 1 HET ZN A 407 1 HET HEM B 401 43 HET HEM B 402 43 HET DMU B 403 12 HET DMU B 404 12 HET DMU B 405 12 HET ZN B 406 1 HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM PE5 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL HETNAM DMU DECYL-BETA-D-MALTOPYRANOSIDE HETNAM ZN ZINC ION HETSYN HEM HEME HETSYN PE5 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}- HETSYN 2 PE5 ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL; POLYETHYLENE HETSYN 3 PE5 GLYCOL PEG400 HETSYN DMU DECYLMALTOSIDE FORMUL 3 HEM 4(C34 H32 FE N4 O4) FORMUL 5 PE5 C18 H38 O9 FORMUL 6 DMU 5(C22 H42 O11) FORMUL 8 ZN 3(ZN 2+) HELIX 1 AA1 ARG A 2 LEU A 30 1 29 HELIX 2 AA2 PHE A 32 ASN A 41 1 10 HELIX 3 AA3 PRO A 42 ALA A 46 5 5 HELIX 4 AA4 SER A 55 TYR A 67 1 13 HELIX 5 AA5 ASN A 127 ASN A 138 1 12 HELIX 6 AA6 GLY A 146 THR A 168 1 23 HELIX 7 AA7 ALA A 190 ALA A 200 1 11 HELIX 8 AA8 GLY A 201 LEU A 221 1 21 HELIX 9 AA9 VAL A 225 SER A 231 1 7 HELIX 10 AB1 SER A 239 ARG A 246 1 8 HELIX 11 AB2 PRO A 248 GLY A 253 5 6 HELIX 12 AB3 ASP A 258 GLY A 274 1 17 HELIX 13 AB4 SER A 326 LEU A 334 1 9 HELIX 14 AB5 LEU A 334 GLY A 340 1 7 HELIX 15 AB6 GLY A 341 ILE A 343 5 3 HELIX 16 AB7 ALA A 344 ARG A 375 1 32 HELIX 17 AB8 ARG B 2 THR B 16 1 15 HELIX 18 AB9 THR B 16 LEU B 30 1 15 HELIX 19 AC1 PHE B 32 ASN B 41 1 10 HELIX 20 AC2 PRO B 42 ALA B 46 5 5 HELIX 21 AC3 SER B 55 TYR B 67 1 13 HELIX 22 AC4 LEU B 128 LEU B 139 1 12 HELIX 23 AC5 GLY B 146 THR B 168 1 23 HELIX 24 AC6 ALA B 190 ALA B 200 1 11 HELIX 25 AC7 GLY B 202 LEU B 221 1 20 HELIX 26 AC8 VAL B 225 SER B 231 1 7 HELIX 27 AC9 SER B 239 ARG B 246 1 8 HELIX 28 AD1 PRO B 248 GLY B 253 5 6 HELIX 29 AD2 ASP B 258 GLY B 274 1 17 HELIX 30 AD3 ASP B 300 LYS B 304 5 5 HELIX 31 AD4 GLY B 328 ARG B 333 1 6 HELIX 32 AD5 LEU B 334 GLY B 341 1 8 HELIX 33 AD6 ALA B 344 HIS B 378 1 35 HELIX 34 AD7 TRP B 379 GLY B 381 5 3 SHEET 1 AA1 8 GLU A 112 ARG A 116 0 SHEET 2 AA1 8 VAL A 102 LEU A 105 -1 N TYR A 104 O VAL A 113 SHEET 3 AA1 8 ALA A 85 PRO A 91 -1 N LEU A 87 O PHE A 103 SHEET 4 AA1 8 GLN A 70 GLU A 76 -1 N TYR A 74 O ALA A 88 SHEET 5 AA1 8 ILE A 279 SER A 285 -1 O TYR A 284 N TRP A 73 SHEET 6 AA1 8 PHE A 290 PHE A 295 -1 O GLY A 292 N TYR A 283 SHEET 7 AA1 8 SER A 305 HIS A 310 -1 O PHE A 309 N PHE A 291 SHEET 8 AA1 8 LEU A 316 GLU A 320 -1 O GLU A 320 N TRP A 306 SHEET 1 AA2 8 GLU B 112 ARG B 116 0 SHEET 2 AA2 8 VAL B 102 LEU B 105 -1 N TYR B 104 O VAL B 113 SHEET 3 AA2 8 ALA B 85 PRO B 91 -1 N LEU B 87 O PHE B 103 SHEET 4 AA2 8 GLN B 70 GLU B 76 -1 N LEU B 71 O VAL B 90 SHEET 5 AA2 8 ILE B 279 SER B 285 -1 O LEU B 282 N MET B 75 SHEET 6 AA2 8 PHE B 290 PHE B 295 -1 O GLY B 292 N TYR B 283 SHEET 7 AA2 8 SER B 305 HIS B 310 -1 O LEU B 307 N ALA B 293 SHEET 8 AA2 8 LEU B 316 GLN B 319 -1 O LEU B 317 N PHE B 308 LINK NE2 HIS A 9 FE HEM A 401 1555 1555 2.52 LINK NE2 HIS A 33 ZN ZN A 406 1555 1555 2.52 LINK NE2 HIS A 34 ZN ZN A 407 1555 1555 2.36 LINK NE2 HIS A 83 ZN ZN A 407 1555 1555 2.49 LINK NE2 HIS A 136 FE HEM A 402 1555 1555 2.11 LINK NE2 HIS A 198 FE HEM A 401 1555 1555 2.22 LINK NE2 HIS A 339 FE HEM A 402 1555 1555 2.14 LINK NE2 HIS B 9 FE HEM B 401 1555 1555 2.18 LINK NE2 HIS B 136 FE HEM B 402 1555 1555 2.29 LINK NE2 HIS B 198 FE HEM B 401 1555 1555 2.16 LINK NE2 HIS B 339 FE HEM B 402 1555 1555 2.54 CRYST1 237.065 114.321 64.382 90.00 90.00 90.00 P 21 21 2 8 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 0.004218 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008747 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015532 0.00000