HEADER TRANSFERASE 16-OCT-17 5YKR TITLE CRYSTAL STRUCTURE OF A GLUTAMATE-1-SEMIALDEHYDE-AMINOMUTASE FROM TITLE 2 PSEUDOMONAS AERUGINOSA PAO1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE AMINOTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GLUTAMATE-1-SEMIALDEHYDE-AMINOMUTASE; COMPND 5 EC: 5.4.3.8; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA (STRAIN ATCC 15692 / DSM SOURCE 3 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1); SOURCE 4 ORGANISM_TAXID: 208964; SOURCE 5 STRAIN: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 SOURCE 6 / 1C / PRS 101 / PAO1; SOURCE 7 GENE: PA4088; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS GLUTAMATE-1-SEMIALDEHYDE-AMINOMUTASE, C5 PATHWAY, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.LI,Q.ZHANG,M.BARTLAM REVDAT 2 22-NOV-23 5YKR 1 REMARK REVDAT 1 26-SEP-18 5YKR 0 JRNL AUTH S.LI,X.LOU,Y.XU,X.TENG,S.CHE,R.LIU,M.BARTLAM JRNL TITL CRYSTAL STRUCTURE OF A GLUTAMATE-1-SEMIALDEHYDE-AMINOMUTASE JRNL TITL 2 FROM PSEUDOMONAS AERUGINOSA PAO1. JRNL REF BIOCHEM. BIOPHYS. RES. V. 500 804 2018 JRNL REF 2 COMMUN. JRNL REFN ESSN 1090-2104 JRNL PMID 29684343 JRNL DOI 10.1016/J.BBRC.2018.04.163 REMARK 2 REMARK 2 RESOLUTION. 1.44 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0173 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 146473 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) : 0.122 REMARK 3 R VALUE (WORKING SET) : 0.120 REMARK 3 FREE R VALUE : 0.155 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 7471 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) : 1.44 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.48 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8929 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 475 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7086 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 963 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : 0.12000 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): 0.059 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.054 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.035 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.090 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7306 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6650 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9938 ; 1.629 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15284 ; 1.050 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 916 ; 6.473 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 358 ;31.515 ;22.291 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1108 ;11.858 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 78 ;17.361 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1068 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8372 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1656 ; 0.002 ; 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): 3652 ; 1.315 ; 1.411 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3651 ; 1.314 ; 1.411 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4572 ; 1.696 ; 2.125 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4573 ; 1.697 ; 2.125 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3654 ; 2.101 ; 1.758 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3655 ; 2.101 ; 1.758 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5367 ; 2.578 ; 2.525 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 8570 ; 3.425 ;19.191 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 8296 ; 2.925 ;18.227 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 13956 ; 2.612 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 616 ;26.439 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 14119 ; 9.966 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 5 457 B 5 457 29920 0.07 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.00 REMARK 3 ION PROBE RADIUS : 0.70 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5YKR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1300005456. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-MAR-16 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 155189 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 3BS8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM SULFATE, 0.1M BIS-TRIS REMARK 280 PH 6.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K 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 44.72100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.17450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.24850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.17450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.72100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.24850 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -58.0 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 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 MET A 1 REMARK 465 ASP A 2 REMARK 465 THR A 3 REMARK 465 THR A 4 REMARK 465 GLU A 458 REMARK 465 ARG A 459 REMARK 465 PRO A 460 REMARK 465 SER A 461 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 THR B 3 REMARK 465 THR B 4 REMARK 465 GLU B 458 REMARK 465 ARG B 459 REMARK 465 PRO B 460 REMARK 465 SER B 461 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 562 O HOH A 624 1.92 REMARK 500 O HOH B 700 O HOH B 846 2.02 REMARK 500 O HOH A 548 O HOH A 624 2.03 REMARK 500 O HOH B 509 O HOH B 512 2.04 REMARK 500 O HOH A 741 O HOH A 812 2.05 REMARK 500 O HOH A 510 O HOH A 884 2.09 REMARK 500 O HOH B 928 O HOH B 973 2.11 REMARK 500 O LEU B 457 O HOH B 501 2.11 REMARK 500 O HOH A 840 O HOH A 855 2.13 REMARK 500 O HOH B 835 O HOH B 879 2.14 REMARK 500 O HOH B 789 O HOH B 920 2.17 REMARK 500 ND1 HIS A 40 O HOH A 501 2.18 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 102 NE - CZ - NH1 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 102 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 144 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 68 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 102 NE - CZ - NH1 ANGL. DEV. = 3.1 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 SER A 85 -10.62 82.20 REMARK 500 VAL A 232 47.61 -150.14 REMARK 500 LLP A 286 -69.39 65.85 REMARK 500 ASN A 429 48.52 -107.15 REMARK 500 SER B 85 -9.05 81.22 REMARK 500 VAL B 232 46.57 -149.55 REMARK 500 LLP B 286 -66.09 62.33 REMARK 500 ASN B 429 48.73 -106.95 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 186 0.10 SIDE CHAIN REMARK 500 ARG B 186 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 982 DISTANCE = 6.73 ANGSTROMS REMARK 525 HOH B 977 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH B 978 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH B 979 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH B 980 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH B 981 DISTANCE = 6.29 ANGSTROMS DBREF 5YKR A 1 461 UNP Q9HWU0 Q9HWU0_PSEAE 1 461 DBREF 5YKR B 1 461 UNP Q9HWU0 Q9HWU0_PSEAE 1 461 SEQRES 1 A 461 MET ASP THR THR PHE GLY LEU ASP LEU ALA ARG VAL GLU SEQRES 2 A 461 THR LEU PHE LYS ARG GLU LEU ARG ARG PHE ASP GLU LEU SEQRES 3 A 461 HIS PRO ARG SER ALA GLN ALA TYR ARG GLU ASN ARG ARG SEQRES 4 A 461 HIS TRP LEU TYR GLY ALA PRO LEU HIS TRP MET GLN GLN SEQRES 5 A 461 TRP PRO GLY ASN CYS PRO LEU LEU VAL LYS GLU ALA GLN SEQRES 6 A 461 GLY ALA ARG VAL THR ASP ILE ASP GLY GLN GLN TYR VAL SEQRES 7 A 461 ASP PHE ALA LEU GLY ASP SER GLY ALA MET PHE GLY HIS SEQRES 8 A 461 ALA GLN PRO ALA VAL ALA ASP ALA ILE ALA ARG GLN ALA SEQRES 9 A 461 ARG ARG GLY SER THR LEU MET LEU PRO THR GLU ASP SER SEQRES 10 A 461 LEU TRP VAL GLY ALA GLU LEU ALA ARG ARG PHE GLY LEU SEQRES 11 A 461 PRO TYR TRP GLN VAL THR THR SER ALA THR ASP ALA ASN SEQRES 12 A 461 ARG PHE VAL LEU ARG LEU CYS ARG MET LEU SER GLY ARG SEQRES 13 A 461 ASP LYS VAL VAL VAL PHE ASN CYS ASN TYR HIS GLY SER SEQRES 14 A 461 VAL ASP GLU SER GLN VAL GLU PHE ASP ALA ALA GLY ARG SEQRES 15 A 461 MET VAL PRO ARG ALA GLY VAL HIS PRO ASN GLY VAL ARG SEQRES 16 A 461 HIS ALA THR THR THR ARG LEU VAL GLU PHE ASN ASP LEU SEQRES 17 A 461 ASP ALA LEU GLU ALA ALA LEU ALA HIS GLY ASP VAL ALA SEQRES 18 A 461 ALA VAL LEU THR GLU PRO PHE MET THR ASN VAL GLY MET SEQRES 19 A 461 VAL PRO PRO ALA GLU GLY PHE HIS ALA GLY LEU ARG GLU SEQRES 20 A 461 LEU THR ARG ARG HIS ASP VAL ALA LEU ILE ILE ASP GLU SEQRES 21 A 461 THR HIS THR ILE SER CYS GLY PRO ALA GLY TYR SER GLY SEQRES 22 A 461 ALA HIS GLY LEU GLU PRO ASP PHE PHE VAL LEU GLY LLP SEQRES 23 A 461 CYS ILE ALA GLY GLY ILE PRO SER ALA VAL TRP GLY CYS SEQRES 24 A 461 SER GLN ALA GLN ALA GLU ARG ILE TRP ALA VAL LEU PRO SEQRES 25 A 461 HIS PHE ARG PRO GLY GLN ALA ILE ASN HIS PHE GLY PHE SEQRES 26 A 461 GLY GLY THR LEU ALA GLY ASN ALA LEU GLN LEU ALA ALA SEQRES 27 A 461 MET ARG ALA THR PHE ALA GLU VAL MET THR GLU ASP ALA SEQRES 28 A 461 TYR ARG HIS MET PHE GLN LEU ALA ALA GLN LEU GLU ALA SEQRES 29 A 461 GLY VAL ARG ALA THR LEU GLU GLU LEU ARG LEU PRO TRP SEQRES 30 A 461 HIS VAL THR ARG ILE GLY ALA ARG VAL GLU TYR LEU PHE SEQRES 31 A 461 MET THR HIS ALA PRO ARG ASN GLY GLY GLU ALA HIS HIS SEQRES 32 A 461 ALA ARG ASN GLY LEU ILE GLU ALA CYS LEU HIS LEU TYR SEQRES 33 A 461 LEU LEU ASN ARG GLY VAL LEU LEU THR PRO PHE HIS ASN SEQRES 34 A 461 MET ALA LEU THR CYS PRO ALA THR ARG ALA GLU ASP VAL SEQRES 35 A 461 GLU LEU HIS ASP ARG LEU LEU ARG ASP CYS LEU GLY GLU SEQRES 36 A 461 LEU LEU GLU ARG PRO SER SEQRES 1 B 461 MET ASP THR THR PHE GLY LEU ASP LEU ALA ARG VAL GLU SEQRES 2 B 461 THR LEU PHE LYS ARG GLU LEU ARG ARG PHE ASP GLU LEU SEQRES 3 B 461 HIS PRO ARG SER ALA GLN ALA TYR ARG GLU ASN ARG ARG SEQRES 4 B 461 HIS TRP LEU TYR GLY ALA PRO LEU HIS TRP MET GLN GLN SEQRES 5 B 461 TRP PRO GLY ASN CYS PRO LEU LEU VAL LYS GLU ALA GLN SEQRES 6 B 461 GLY ALA ARG VAL THR ASP ILE ASP GLY GLN GLN TYR VAL SEQRES 7 B 461 ASP PHE ALA LEU GLY ASP SER GLY ALA MET PHE GLY HIS SEQRES 8 B 461 ALA GLN PRO ALA VAL ALA ASP ALA ILE ALA ARG GLN ALA SEQRES 9 B 461 ARG ARG GLY SER THR LEU MET LEU PRO THR GLU ASP SER SEQRES 10 B 461 LEU TRP VAL GLY ALA GLU LEU ALA ARG ARG PHE GLY LEU SEQRES 11 B 461 PRO TYR TRP GLN VAL THR THR SER ALA THR ASP ALA ASN SEQRES 12 B 461 ARG PHE VAL LEU ARG LEU CYS ARG MET LEU SER GLY ARG SEQRES 13 B 461 ASP LYS VAL VAL VAL PHE ASN CYS ASN TYR HIS GLY SER SEQRES 14 B 461 VAL ASP GLU SER GLN VAL GLU PHE ASP ALA ALA GLY ARG SEQRES 15 B 461 MET VAL PRO ARG ALA GLY VAL HIS PRO ASN GLY VAL ARG SEQRES 16 B 461 HIS ALA THR THR THR ARG LEU VAL GLU PHE ASN ASP LEU SEQRES 17 B 461 ASP ALA LEU GLU ALA ALA LEU ALA HIS GLY ASP VAL ALA SEQRES 18 B 461 ALA VAL LEU THR GLU PRO PHE MET THR ASN VAL GLY MET SEQRES 19 B 461 VAL PRO PRO ALA GLU GLY PHE HIS ALA GLY LEU ARG GLU SEQRES 20 B 461 LEU THR ARG ARG HIS ASP VAL ALA LEU ILE ILE ASP GLU SEQRES 21 B 461 THR HIS THR ILE SER CYS GLY PRO ALA GLY TYR SER GLY SEQRES 22 B 461 ALA HIS GLY LEU GLU PRO ASP PHE PHE VAL LEU GLY LLP SEQRES 23 B 461 CYS ILE ALA GLY GLY ILE PRO SER ALA VAL TRP GLY CYS SEQRES 24 B 461 SER GLN ALA GLN ALA GLU ARG ILE TRP ALA VAL LEU PRO SEQRES 25 B 461 HIS PHE ARG PRO GLY GLN ALA ILE ASN HIS PHE GLY PHE SEQRES 26 B 461 GLY GLY THR LEU ALA GLY ASN ALA LEU GLN LEU ALA ALA SEQRES 27 B 461 MET ARG ALA THR PHE ALA GLU VAL MET THR GLU ASP ALA SEQRES 28 B 461 TYR ARG HIS MET PHE GLN LEU ALA ALA GLN LEU GLU ALA SEQRES 29 B 461 GLY VAL ARG ALA THR LEU GLU GLU LEU ARG LEU PRO TRP SEQRES 30 B 461 HIS VAL THR ARG ILE GLY ALA ARG VAL GLU TYR LEU PHE SEQRES 31 B 461 MET THR HIS ALA PRO ARG ASN GLY GLY GLU ALA HIS HIS SEQRES 32 B 461 ALA ARG ASN GLY LEU ILE GLU ALA CYS LEU HIS LEU TYR SEQRES 33 B 461 LEU LEU ASN ARG GLY VAL LEU LEU THR PRO PHE HIS ASN SEQRES 34 B 461 MET ALA LEU THR CYS PRO ALA THR ARG ALA GLU ASP VAL SEQRES 35 B 461 GLU LEU HIS ASP ARG LEU LEU ARG ASP CYS LEU GLY GLU SEQRES 36 B 461 LEU LEU GLU ARG PRO SER MODRES 5YKR LLP A 286 LYS MODIFIED RESIDUE MODRES 5YKR LLP B 286 LYS MODIFIED RESIDUE HET LLP A 286 24 HET LLP B 286 24 HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE FORMUL 1 LLP 2(C14 H22 N3 O7 P) FORMUL 3 HOH *963(H2 O) HELIX 1 AA1 ASP A 8 HIS A 27 1 20 HELIX 2 AA2 HIS A 27 ARG A 38 1 12 HELIX 3 AA3 LEU A 47 TRP A 53 5 7 HELIX 4 AA4 GLN A 93 ARG A 105 1 13 HELIX 5 AA5 THR A 114 GLY A 129 1 16 HELIX 6 AA6 SER A 138 GLY A 155 1 18 HELIX 7 AA7 VAL A 170 SER A 173 5 4 HELIX 8 AA8 ARG A 195 THR A 198 5 4 HELIX 9 AA9 ASP A 207 ALA A 216 1 10 HELIX 10 AB1 GLY A 240 HIS A 252 1 13 HELIX 11 AB2 HIS A 262 GLY A 267 5 6 HELIX 12 AB3 ALA A 269 GLY A 276 1 8 HELIX 13 AB4 SER A 300 LEU A 311 1 12 HELIX 14 AB5 ASN A 332 VAL A 346 1 15 HELIX 15 AB6 THR A 348 LEU A 373 1 26 HELIX 16 AB7 ASN A 397 HIS A 403 1 7 HELIX 17 AB8 ASN A 406 ASN A 419 1 14 HELIX 18 AB9 ARG A 438 LEU A 457 1 20 HELIX 19 AC1 ASP B 8 HIS B 27 1 20 HELIX 20 AC2 HIS B 27 TRP B 41 1 15 HELIX 21 AC3 LEU B 47 TRP B 53 5 7 HELIX 22 AC4 GLN B 93 ARG B 105 1 13 HELIX 23 AC5 THR B 114 GLY B 129 1 16 HELIX 24 AC6 SER B 138 GLY B 155 1 18 HELIX 25 AC7 VAL B 170 SER B 173 5 4 HELIX 26 AC8 ARG B 195 THR B 198 5 4 HELIX 27 AC9 ASP B 207 ALA B 216 1 10 HELIX 28 AD1 GLY B 240 HIS B 252 1 13 HELIX 29 AD2 HIS B 262 GLY B 267 5 6 HELIX 30 AD3 ALA B 269 GLY B 276 1 8 HELIX 31 AD4 SER B 300 LEU B 311 1 12 HELIX 32 AD5 ASN B 332 VAL B 346 1 15 HELIX 33 AD6 THR B 348 ARG B 374 1 27 HELIX 34 AD7 ASN B 397 HIS B 403 1 7 HELIX 35 AD8 ASN B 406 ASN B 419 1 14 HELIX 36 AD9 ARG B 438 LEU B 457 1 20 SHEET 1 AA1 4 VAL A 61 GLN A 65 0 SHEET 2 AA1 4 ARG A 68 ASP A 71 -1 O THR A 70 N GLU A 63 SHEET 3 AA1 4 GLN A 76 ASP A 79 -1 O TYR A 77 N VAL A 69 SHEET 4 AA1 4 VAL A 422 LEU A 423 1 O LEU A 423 N VAL A 78 SHEET 1 AA2 7 TYR A 132 THR A 136 0 SHEET 2 AA2 7 ALA A 295 CYS A 299 -1 O ALA A 295 N THR A 136 SHEET 3 AA2 7 PHE A 281 GLY A 285 -1 N LEU A 284 O VAL A 296 SHEET 4 AA2 7 ALA A 255 ASP A 259 1 N ILE A 258 O PHE A 281 SHEET 5 AA2 7 VAL A 220 THR A 225 1 N VAL A 223 O ILE A 257 SHEET 6 AA2 7 LYS A 158 PHE A 162 1 N LYS A 158 O ALA A 221 SHEET 7 AA2 7 THR A 200 VAL A 203 1 O ARG A 201 N VAL A 159 SHEET 1 AA3 2 VAL A 175 PHE A 177 0 SHEET 2 AA3 2 MET A 183 PRO A 185 -1 O VAL A 184 N GLU A 176 SHEET 1 AA4 3 HIS A 378 ILE A 382 0 SHEET 2 AA4 3 ARG A 385 LEU A 389 -1 O ARG A 385 N ILE A 382 SHEET 3 AA4 3 MET A 430 LEU A 432 -1 O ALA A 431 N VAL A 386 SHEET 1 AA5 4 VAL B 61 GLN B 65 0 SHEET 2 AA5 4 ARG B 68 ASP B 71 -1 O THR B 70 N GLU B 63 SHEET 3 AA5 4 GLN B 76 ASP B 79 -1 O TYR B 77 N VAL B 69 SHEET 4 AA5 4 VAL B 422 LEU B 423 1 O LEU B 423 N VAL B 78 SHEET 1 AA6 7 TYR B 132 THR B 136 0 SHEET 2 AA6 7 ALA B 295 CYS B 299 -1 O ALA B 295 N THR B 136 SHEET 3 AA6 7 PHE B 281 LEU B 284 -1 N LEU B 284 O VAL B 296 SHEET 4 AA6 7 ALA B 255 ASP B 259 1 N ILE B 258 O PHE B 281 SHEET 5 AA6 7 VAL B 220 THR B 225 1 N VAL B 223 O ILE B 257 SHEET 6 AA6 7 LYS B 158 PHE B 162 1 N LYS B 158 O ALA B 221 SHEET 7 AA6 7 THR B 200 VAL B 203 1 O ARG B 201 N VAL B 159 SHEET 1 AA7 2 VAL B 175 PHE B 177 0 SHEET 2 AA7 2 MET B 183 PRO B 185 -1 O VAL B 184 N GLU B 176 SHEET 1 AA8 3 HIS B 378 ILE B 382 0 SHEET 2 AA8 3 ARG B 385 LEU B 389 -1 O GLU B 387 N THR B 380 SHEET 3 AA8 3 MET B 430 LEU B 432 -1 O ALA B 431 N VAL B 386 LINK C GLY A 285 N LLP A 286 1555 1555 1.35 LINK C LLP A 286 N CYS A 287 1555 1555 1.32 LINK C GLY B 285 N LLP B 286 1555 1555 1.34 LINK C LLP B 286 N CYS B 287 1555 1555 1.32 CRYST1 89.442 96.497 100.349 90.00 90.00 90.00 P 21 21 21 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 0.011180 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010363 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009965 0.00000