HEADER TRANSFERASE 15-JUL-10 3NYT TITLE X-RAY CRYSTAL STRUCTURE OF THE WLBE (WPBE) AMINOTRANSFERASE FROM TITLE 2 PSEUDOMONAS AERUGINOSA, MUTATION K185A, IN COMPLEX WITH THE PLP TITLE 3 EXTERNAL ALDIMINE ADDUCT WITH UDP-3-AMINO-2-N-ACETYL-GLUCURONIC ACID, TITLE 4 AT 1.3 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINOTRANSFERASE WBPE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 STRAIN: PAO1; SOURCE 5 GENE: PA3155, WBPE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET31 KEYWDS AMINOTRANSFERASE, PLP BINDING, NUCLEOTIDE-SUGAR BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR H.M.HOLDEN,J.B.THODEN REVDAT 4 06-SEP-23 3NYT 1 REMARK SEQADV LINK REVDAT 3 29-MAR-17 3NYT 1 JRNL REVDAT 2 11-JAN-17 3NYT 1 JRNL VERSN REVDAT 1 28-JUL-10 3NYT 0 JRNL AUTH G.T.DOW,M.GILBERT,J.B.THODEN,H.M.HOLDEN JRNL TITL STRUCTURAL INVESTIGATION ON WLARG FROM CAMPYLOBACTER JEJUNI: JRNL TITL 2 A SUGAR AMINOTRANSFERASE. JRNL REF PROTEIN SCI. V. 26 586 2017 JRNL REFN ISSN 0961-8368 JRNL PMID 28028852 JRNL DOI 10.1002/PRO.3109 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0066 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 86156 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4537 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.34 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5827 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.96 REMARK 3 BIN R VALUE (WORKING SET) : 0.3640 REMARK 3 BIN FREE R VALUE SET COUNT : 284 REMARK 3 BIN FREE R VALUE : 0.3840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2729 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.03000 REMARK 3 B33 (A**2) : -0.48000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.61000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.053 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.056 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.037 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.900 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2854 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3896 ; 2.180 ; 1.998 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 364 ; 6.262 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 118 ;33.325 ;24.661 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 465 ;12.576 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;20.342 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 454 ; 0.146 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2146 ; 0.013 ; 0.021 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): 1799 ; 1.519 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2906 ; 2.288 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1055 ; 3.515 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 987 ; 5.455 ; 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 : 1.40 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 3NYT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000060449. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 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 : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NI-FILTER REMARK 200 OPTICS : MONTEL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRUKER PLATINUM 135 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SAINT REMARK 200 DATA SCALING SOFTWARE : SADABS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 90696 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : 0.05100 REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.33000 REMARK 200 R SYM FOR SHELL (I) : 0.33000 REMARK 200 FOR SHELL : 3.000 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: PDB ENTRY 3NYS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PENTAERYTHRITOL PROPOXYLATE, 100 REMARK 280 MM MES, 50MM UDP-3-AMINO-20N-ACETYL-GLUCURONIC ACID, PH 6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 29.84200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.08500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.84200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 46.08500 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: 5370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL 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 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 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 557 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 588 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 683 LIES ON A SPECIAL POSITION. 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 LEU A 360 REMARK 465 GLU A 361 REMARK 465 HIS A 362 REMARK 465 HIS A 363 REMARK 465 HIS A 364 REMARK 465 HIS A 365 REMARK 465 HIS A 366 REMARK 465 HIS A 367 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 ASN A 359 CG OD1 ND2 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 404 O HOH A 445 1.98 REMARK 500 O HOH A 446 O HOH A 447 1.99 REMARK 500 NZ LYS A 125 O HOH A 726 2.15 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 A 408 O HOH A 456 2656 2.07 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 ASP A 16 CB - CG - OD1 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 27 CD - NE - CZ ANGL. DEV. = 8.8 DEGREES REMARK 500 ARG A 27 NE - CZ - NH1 ANGL. DEV. = -9.2 DEGREES REMARK 500 ARG A 27 NE - CZ - NH2 ANGL. DEV. = 8.2 DEGREES REMARK 500 ASP A 103 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 107 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 107 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 201 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 212 NE - CZ - NH2 ANGL. DEV. = 7.2 DEGREES REMARK 500 TYR A 281 CB - CG - CD1 ANGL. DEV. = -4.2 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 ILE A 128 79.64 -119.47 REMARK 500 CYS A 171 -4.76 89.93 REMARK 500 TYR A 190 55.64 -115.28 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 NA A 369 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 528 O REMARK 620 2 HOH A 534 O 89.2 REMARK 620 3 HOH A 569 O 84.0 84.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ULP A 368 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 369 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NYS RELATED DB: PDB REMARK 900 SAME PROTEIN, K185A MUTATION, PLP LIGAND REMARK 900 RELATED ID: 3NYU RELATED DB: PDB REMARK 900 SAME PROTEIN, WITH PLP INTERNAL ALDIMINE ADDUCT DBREF 3NYT A 1 359 UNP Q9HZ76 Q9HZ76_PSEAE 1 359 SEQADV 3NYT ALA A 185 UNP Q9HZ76 LYS 185 ENGINEERED MUTATION SEQADV 3NYT LEU A 360 UNP Q9HZ76 EXPRESSION TAG SEQADV 3NYT GLU A 361 UNP Q9HZ76 EXPRESSION TAG SEQADV 3NYT HIS A 362 UNP Q9HZ76 EXPRESSION TAG SEQADV 3NYT HIS A 363 UNP Q9HZ76 EXPRESSION TAG SEQADV 3NYT HIS A 364 UNP Q9HZ76 EXPRESSION TAG SEQADV 3NYT HIS A 365 UNP Q9HZ76 EXPRESSION TAG SEQADV 3NYT HIS A 366 UNP Q9HZ76 EXPRESSION TAG SEQADV 3NYT HIS A 367 UNP Q9HZ76 EXPRESSION TAG SEQRES 1 A 367 MET ILE GLU PHE ILE ASP LEU LYS ASN GLN GLN ALA ARG SEQRES 2 A 367 ILE LYS ASP LYS ILE ASP ALA GLY ILE GLN ARG VAL LEU SEQRES 3 A 367 ARG HIS GLY GLN TYR ILE LEU GLY PRO GLU VAL THR GLU SEQRES 4 A 367 LEU GLU ASP ARG LEU ALA ASP PHE VAL GLY ALA LYS TYR SEQRES 5 A 367 CYS ILE SER CYS ALA ASN GLY THR ASP ALA LEU GLN ILE SEQRES 6 A 367 VAL GLN MET ALA LEU GLY VAL GLY PRO GLY ASP GLU VAL SEQRES 7 A 367 ILE THR PRO GLY PHE THR TYR VAL ALA THR ALA GLU THR SEQRES 8 A 367 VAL ALA LEU LEU GLY ALA LYS PRO VAL TYR VAL ASP ILE SEQRES 9 A 367 ASP PRO ARG THR TYR ASN LEU ASP PRO GLN LEU LEU GLU SEQRES 10 A 367 ALA ALA ILE THR PRO ARG THR LYS ALA ILE ILE PRO VAL SEQRES 11 A 367 SER LEU TYR GLY GLN CYS ALA ASP PHE ASP ALA ILE ASN SEQRES 12 A 367 ALA ILE ALA SER LYS TYR GLY ILE PRO VAL ILE GLU ASP SEQRES 13 A 367 ALA ALA GLN SER PHE GLY ALA SER TYR LYS GLY LYS ARG SEQRES 14 A 367 SER CYS ASN LEU SER THR VAL ALA CYS THR SER PHE PHE SEQRES 15 A 367 PRO SER ALA PRO LEU GLY CYS TYR GLY ASP GLY GLY ALA SEQRES 16 A 367 ILE PHE THR ASN ASP ASP GLU LEU ALA THR ALA ILE ARG SEQRES 17 A 367 GLN ILE ALA ARG HIS GLY GLN ASP ARG ARG TYR HIS HIS SEQRES 18 A 367 ILE ARG VAL GLY VAL ASN SER ARG LEU ASP THR LEU GLN SEQRES 19 A 367 ALA ALA ILE LEU LEU PRO LYS LEU GLU ILE PHE GLU GLU SEQRES 20 A 367 GLU ILE ALA LEU ARG GLN LYS VAL ALA ALA GLU TYR ASP SEQRES 21 A 367 LEU SER LEU LYS GLN VAL GLY ILE GLY THR PRO PHE ILE SEQRES 22 A 367 GLU VAL ASN ASN ILE SER VAL TYR ALA GLN TYR THR VAL SEQRES 23 A 367 ARG MET ASP ASN ARG GLU SER VAL GLN ALA SER LEU LYS SEQRES 24 A 367 ALA ALA GLY VAL PRO THR ALA VAL HIS TYR PRO ILE PRO SEQRES 25 A 367 LEU ASN LYS GLN PRO ALA VAL ALA ASP GLU LYS ALA LYS SEQRES 26 A 367 LEU PRO VAL GLY ASP LYS ALA ALA THR GLN VAL MET SER SEQRES 27 A 367 LEU PRO MET HIS PRO TYR LEU ASP THR ALA SER ILE LYS SEQRES 28 A 367 ILE ILE CYS ALA ALA LEU THR ASN LEU GLU HIS HIS HIS SEQRES 29 A 367 HIS HIS HIS HET ULP A 368 55 HET NA A 369 1 HETNAM ULP (2S,3S,4R,5R,6R)-5-(ACETYLAMINO)-6-{[(R)-{[(S)-{[(2R, HETNAM 2 ULP 3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)- HETNAM 3 ULP 3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY) HETNAM 4 ULP PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-3-HYDROXY-4- HETNAM 5 ULP {[(1E)-{3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY) HETNAM 6 ULP METHYL]PYRIDIN-4-YL}METHYLIDENE]AMINO}TETRAHYDRO-2H- HETNAM 7 ULP PYRAN-2-CARBOXYLIC ACID (NON-PREFERRED NAME) HETNAM NA SODIUM ION FORMUL 2 ULP C25 H34 N5 O22 P3 FORMUL 3 NA NA 1+ FORMUL 4 HOH *470(H2 O) HELIX 1 1 LEU A 7 GLY A 29 1 23 HELIX 2 2 GLY A 34 GLY A 49 1 16 HELIX 3 3 ASN A 58 LEU A 70 1 13 HELIX 4 4 VAL A 86 LEU A 95 1 10 HELIX 5 5 ASP A 112 ILE A 120 5 9 HELIX 6 6 SER A 131 GLN A 135 5 5 HELIX 7 7 ASP A 138 TYR A 149 1 12 HELIX 8 8 ASP A 200 ALA A 211 1 12 HELIX 9 9 ASP A 231 ILE A 244 1 14 HELIX 10 10 ILE A 244 VAL A 266 1 23 HELIX 11 11 ASN A 290 GLY A 302 1 13 HELIX 12 12 PRO A 312 ALA A 320 5 9 HELIX 13 13 LEU A 326 GLN A 335 1 10 HELIX 14 14 ASP A 346 ASN A 359 1 14 SHEET 1 A 4 TYR A 52 CYS A 56 0 SHEET 2 A 4 GLY A 194 THR A 198 -1 O ILE A 196 N ILE A 54 SHEET 3 A 4 VAL A 176 SER A 180 -1 N THR A 179 O ALA A 195 SHEET 4 A 4 ILE A 154 ASP A 156 1 N GLU A 155 O CYS A 178 SHEET 1 B 3 LYS A 98 VAL A 102 0 SHEET 2 B 3 GLU A 77 PRO A 81 1 N VAL A 78 O VAL A 100 SHEET 3 B 3 THR A 124 ILE A 127 1 O LYS A 125 N GLU A 77 SHEET 1 C 3 LYS A 168 ARG A 169 0 SHEET 2 C 3 SER A 164 TYR A 165 -1 N TYR A 165 O LYS A 168 SHEET 3 C 3 ASN A 277 ILE A 278 -1 O ILE A 278 N SER A 164 SHEET 1 D 2 GLN A 215 ARG A 217 0 SHEET 2 D 2 HIS A 220 HIS A 221 -1 O HIS A 220 N ARG A 217 SHEET 1 E 2 TYR A 284 ARG A 287 0 SHEET 2 E 2 VAL A 336 LEU A 339 -1 O MET A 337 N VAL A 286 LINK NA NA A 369 O HOH A 528 1555 1555 2.24 LINK NA NA A 369 O HOH A 534 1555 1555 2.08 LINK NA NA A 369 O HOH A 569 1555 1555 2.23 CISPEP 1 HIS A 308 TYR A 309 0 19.32 SITE 1 AC1 35 ILE A 5 LEU A 7 GLY A 29 GLN A 30 SITE 2 AC1 35 TYR A 31 ILE A 32 ASN A 58 GLY A 59 SITE 3 AC1 35 THR A 60 THR A 84 TYR A 85 ALA A 87 SITE 4 AC1 35 VAL A 130 ASP A 156 ALA A 158 GLN A 159 SITE 5 AC1 35 SER A 180 PHE A 182 SER A 184 TYR A 219 SITE 6 AC1 35 ASN A 227 ARG A 229 HIS A 308 TYR A 309 SITE 7 AC1 35 HOH A 488 HOH A 524 HOH A 561 HOH A 601 SITE 8 AC1 35 HOH A 608 HOH A 617 HOH A 639 HOH A 644 SITE 9 AC1 35 HOH A 645 HOH A 786 HOH A 802 SITE 1 AC2 3 HOH A 528 HOH A 534 HOH A 569 CRYST1 59.684 92.170 75.652 90.00 111.84 90.00 C 1 2 1 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016755 0.000000 0.006715 0.00000 SCALE2 0.000000 0.010850 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014241 0.00000