HEADER TRANSFERASE 11-OCT-10 3P6K TITLE CRYSTAL STRUCTURE OF A PLP-DEPENDENT AMINOTRANSFERASE (ZP_03625122.1) TITLE 2 FROM STREPTOCOCCUS SUIS 89-1591 AT 2.07 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMINOTRANSFERASE CLASS I AND II; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS SUIS 89/1591; SOURCE 3 ORGANISM_TAXID: 286604; SOURCE 4 GENE: SSUIDRAFT_2941; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HK100; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: SPEEDET KEYWDS STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, PSI-BIOLOGY, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 3 01-FEB-23 3P6K 1 REMARK SEQADV LINK REVDAT 2 20-JUL-11 3P6K 1 KEYWDS REVDAT 1 27-OCT-10 3P6K 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF A PLP-DEPENDENT AMINOTRANSFERASE JRNL TITL 2 (ZP_03625122.1) FROM STREPTOCOCCUS SUIS 89-1591 AT 2.07 A JRNL TITL 3 RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 44641 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2249 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.12 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3070 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.78 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 168 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5939 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 43 REMARK 3 SOLVENT ATOMS : 305 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.93 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.82000 REMARK 3 B22 (A**2) : 0.82000 REMARK 3 B33 (A**2) : -1.23000 REMARK 3 B12 (A**2) : 0.41000 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): 0.231 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.170 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.127 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.394 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6218 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4110 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8489 ; 1.794 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10070 ; 1.374 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 771 ; 4.306 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 298 ;31.811 ;24.899 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1057 ;11.943 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;15.923 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 949 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6907 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1216 ; 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): 3746 ; 0.624 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1515 ; 0.184 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6082 ; 1.173 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2472 ; 2.018 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2392 ; 3.358 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 3 A 24 6 REMARK 3 1 B 3 B 24 6 REMARK 3 2 A 30 A 371 4 REMARK 3 2 B 30 B 371 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 4443 ; 0.310 ; 0.500 REMARK 3 LOOSE POSITIONAL 1 A (A): 254 ; 0.240 ; 5.000 REMARK 3 MEDIUM THERMAL 1 A (A**2): 4443 ; 0.800 ; 2.000 REMARK 3 LOOSE THERMAL 1 A (A**2): 254 ; 1.620 ;10.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 3 A 371 REMARK 3 ORIGIN FOR THE GROUP (A): 61.5400 19.2340 8.2770 REMARK 3 T TENSOR REMARK 3 T11: 0.1133 T22: 0.1593 REMARK 3 T33: 0.1579 T12: 0.0122 REMARK 3 T13: 0.0018 T23: -0.0581 REMARK 3 L TENSOR REMARK 3 L11: 1.4514 L22: 2.0862 REMARK 3 L33: 2.2940 L12: 1.1103 REMARK 3 L13: 0.8704 L23: 0.8499 REMARK 3 S TENSOR REMARK 3 S11: -0.0698 S12: 0.3930 S13: -0.3373 REMARK 3 S21: -0.3383 S22: 0.2655 S23: -0.2428 REMARK 3 S31: -0.0076 S32: 0.4029 S33: -0.1958 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 374 REMARK 3 ORIGIN FOR THE GROUP (A): 63.0850 27.7620 40.4490 REMARK 3 T TENSOR REMARK 3 T11: 0.0372 T22: 0.0886 REMARK 3 T33: 0.0641 T12: -0.0452 REMARK 3 T13: -0.0127 T23: 0.0401 REMARK 3 L TENSOR REMARK 3 L11: 1.3647 L22: 0.5576 REMARK 3 L33: 1.5503 L12: -0.2228 REMARK 3 L13: 0.5453 L23: -0.0679 REMARK 3 S TENSOR REMARK 3 S11: 0.0218 S12: -0.1997 S13: -0.0720 REMARK 3 S21: -0.0653 S22: 0.0927 S23: 0.0012 REMARK 3 S31: 0.0473 S32: -0.0009 S33: -0.1144 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 1. HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND REMARK 3 RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND REMARK 3 RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS REMARK 3 ASSIGNMENT. 5. A MET-INHIBITION PROTOCOL WAS USED FOR REMARK 3 SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE REMARK 3 OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO REMARK 3 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET REMARK 3 INCORPORATION. 6. SULFATE (SO4) AND 1,2-ETHANEDIOL (EDO) REMARK 3 MOLECULES FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE REMARK 3 MODELED. 7. RESIDUE LYSINE 221 IS COVALENTLY ATTACHED TO REMARK 3 PYRIDOXAL-5'-PHOSPHATE VIA A SCHIFF BASE LINKAGE AND IS MODELED REMARK 3 AS LLP. 8. AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED NEAR RESIDUE REMARK 3 LLP 221. THE UNL RESEMBLES PYRIDOXAMINE (PXM), A POSSIBLE REMARK 3 REACTION PRODUCT OF THE ENZYME. REMARK 4 REMARK 4 3P6K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000062019. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-10 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 : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91162,0.97920,0.97903 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44694 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 29.399 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.51400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELX, SHELXD, AUTOSHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.20M LITHIUM SULFATE 2.00M AMMONIUM REMARK 280 SULFATE, ADDITIVE: 0.001M PYRIDOXAL 5'-PHOSPHATE (PLP), NANODROP, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 117.59400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 58.79700 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 58.79700 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 117.59400 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 300 REMARK: CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER REMARK 300 AS THE SIGNIFICANT OLIGOMERIZATION STATE. 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: 7350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26210 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 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 GLY A 0 REMARK 465 MSE A 1 REMARK 465 LYS A 2 REMARK 465 LYS A 372 REMARK 465 GLU A 373 REMARK 465 ASN A 374 REMARK 465 GLY B 0 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 ARG A 5 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 151 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 200 CG CD OE1 OE2 REMARK 470 GLN A 238 CG CD OE1 NE2 REMARK 470 LYS B 49 CG CD CE NZ REMARK 470 GLN B 238 CG CD OE1 NE2 REMARK 470 GLU B 274 CG CD OE1 OE2 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 B 275 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 369 NE - CZ - NH1 ANGL. DEV. = 3.4 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 29 103.37 -11.09 REMARK 500 MSE A 251 -22.73 -153.45 REMARK 500 ILE A 252 -62.43 66.10 REMARK 500 SER A 306 21.28 -72.13 REMARK 500 MSE B 251 -24.85 -145.95 REMARK 500 ILE B 252 -63.58 64.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 391485 RELATED DB: TARGETDB REMARK 900 RELATED ID: 3OP7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A PLP-DEPENDENT AMINOTRANSFERASE (ZP_ REMARK 900 03625122.1) FROM STREPTOCOCCUS SUIS 89-1591 AT 1.70 A RESOLUTION REMARK 900 (TETRAGONAL FORM) REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG REMARK 999 MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING REMARK 999 ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3P6K A 1 374 UNP B9WVA1 B9WVA1_STRSU 1 374 DBREF 3P6K B 1 374 UNP B9WVA1 B9WVA1_STRSU 1 374 SEQADV 3P6K GLY A 0 UNP B9WVA1 EXPRESSION TAG SEQADV 3P6K GLY B 0 UNP B9WVA1 EXPRESSION TAG SEQRES 1 A 375 GLY MSE LYS LEU PRO ARG PHE GLY VAL GLU GLU TRP LEU SEQRES 2 A 375 ASN VAL HIS GLU ASN SER ALA ILE TYR ASP ILE ALA GLY SEQRES 3 A 375 VAL SER ILE SER SER LEU THR LEU GLU GLU LEU PHE ALA SEQRES 4 A 375 LEU SER GLY THR ASN PRO GLU ASP PHE TYR LYS LYS LEU SEQRES 5 A 375 GLN GLY THR LYS LEU ASN TYR GLY TRP ILE GLU GLY SER SEQRES 6 A 375 PRO ALA PHE LYS LYS SER VAL SER GLN LEU TYR THR GLY SEQRES 7 A 375 VAL LYS PRO GLU GLN ILE LEU GLN THR ASN GLY ALA THR SEQRES 8 A 375 GLY ALA ASN LEU LEU VAL LEU TYR SER LEU ILE GLU PRO SEQRES 9 A 375 GLY ASP HIS VAL ILE SER LEU TYR PRO THR TYR GLN GLN SEQRES 10 A 375 LEU TYR ASP ILE PRO LYS SER LEU GLY ALA GLU VAL ASP SEQRES 11 A 375 LEU TRP GLN ILE GLU GLU GLU ASN GLY TRP LEU PRO ASP SEQRES 12 A 375 LEU GLU LYS LEU ARG GLN LEU ILE ARG PRO THR THR LYS SEQRES 13 A 375 MSE ILE CYS ILE ASN ASN ALA ASN ASN PRO THR GLY ALA SEQRES 14 A 375 VAL MSE ASP ARG THR TYR LEU GLU GLU LEU VAL GLU ILE SEQRES 15 A 375 ALA SER GLU VAL GLY ALA TYR ILE LEU SER ASP GLU VAL SEQRES 16 A 375 TYR ARG SER PHE SER GLU LEU ASP VAL PRO SER ILE ILE SEQRES 17 A 375 GLU VAL TYR ASP LYS GLY ILE ALA VAL ASN SER LEU SER SEQRES 18 A 375 LLP THR TYR SER LEU PRO GLY ILE ARG ILE GLY TRP VAL SEQRES 19 A 375 ALA ALA ASN HIS GLN VAL THR ASP ILE LEU ARG ASP TYR SEQRES 20 A 375 ARG ASP TYR THR MSE ILE CYS ALA GLY VAL PHE ASP ASP SEQRES 21 A 375 LEU VAL ALA GLN LEU ALA LEU ALA HIS TYR GLN GLU ILE SEQRES 22 A 375 LEU GLU ARG ASN ARG HIS ILE LEU GLU GLU ASN LEU ALA SEQRES 23 A 375 ILE LEU ASP GLN TRP ILE GLU GLU GLU PRO LEU VAL SER SEQRES 24 A 375 TYR ILE ARG PRO ALA VAL VAL SER THR SER PHE VAL LYS SEQRES 25 A 375 ILE ALA VAL ASP MSE PRO MSE GLU ASP PHE CYS LEU GLN SEQRES 26 A 375 LEU LEU GLN GLU HIS GLY VAL LEU LEU VAL PRO GLY ASN SEQRES 27 A 375 ARG PHE GLU ARG ASP GLY TYR VAL ARG LEU GLY PHE ALA SEQRES 28 A 375 CYS GLU GLN GLU THR LEU ILE LYS GLY LEU GLU LYS LEU SEQRES 29 A 375 SER GLN PHE LEU ARG ARG PHE ASP LYS GLU ASN SEQRES 1 B 375 GLY MSE LYS LEU PRO ARG PHE GLY VAL GLU GLU TRP LEU SEQRES 2 B 375 ASN VAL HIS GLU ASN SER ALA ILE TYR ASP ILE ALA GLY SEQRES 3 B 375 VAL SER ILE SER SER LEU THR LEU GLU GLU LEU PHE ALA SEQRES 4 B 375 LEU SER GLY THR ASN PRO GLU ASP PHE TYR LYS LYS LEU SEQRES 5 B 375 GLN GLY THR LYS LEU ASN TYR GLY TRP ILE GLU GLY SER SEQRES 6 B 375 PRO ALA PHE LYS LYS SER VAL SER GLN LEU TYR THR GLY SEQRES 7 B 375 VAL LYS PRO GLU GLN ILE LEU GLN THR ASN GLY ALA THR SEQRES 8 B 375 GLY ALA ASN LEU LEU VAL LEU TYR SER LEU ILE GLU PRO SEQRES 9 B 375 GLY ASP HIS VAL ILE SER LEU TYR PRO THR TYR GLN GLN SEQRES 10 B 375 LEU TYR ASP ILE PRO LYS SER LEU GLY ALA GLU VAL ASP SEQRES 11 B 375 LEU TRP GLN ILE GLU GLU GLU ASN GLY TRP LEU PRO ASP SEQRES 12 B 375 LEU GLU LYS LEU ARG GLN LEU ILE ARG PRO THR THR LYS SEQRES 13 B 375 MSE ILE CYS ILE ASN ASN ALA ASN ASN PRO THR GLY ALA SEQRES 14 B 375 VAL MSE ASP ARG THR TYR LEU GLU GLU LEU VAL GLU ILE SEQRES 15 B 375 ALA SER GLU VAL GLY ALA TYR ILE LEU SER ASP GLU VAL SEQRES 16 B 375 TYR ARG SER PHE SER GLU LEU ASP VAL PRO SER ILE ILE SEQRES 17 B 375 GLU VAL TYR ASP LYS GLY ILE ALA VAL ASN SER LEU SER SEQRES 18 B 375 LLP THR TYR SER LEU PRO GLY ILE ARG ILE GLY TRP VAL SEQRES 19 B 375 ALA ALA ASN HIS GLN VAL THR ASP ILE LEU ARG ASP TYR SEQRES 20 B 375 ARG ASP TYR THR MSE ILE CYS ALA GLY VAL PHE ASP ASP SEQRES 21 B 375 LEU VAL ALA GLN LEU ALA LEU ALA HIS TYR GLN GLU ILE SEQRES 22 B 375 LEU GLU ARG ASN ARG HIS ILE LEU GLU GLU ASN LEU ALA SEQRES 23 B 375 ILE LEU ASP GLN TRP ILE GLU GLU GLU PRO LEU VAL SER SEQRES 24 B 375 TYR ILE ARG PRO ALA VAL VAL SER THR SER PHE VAL LYS SEQRES 25 B 375 ILE ALA VAL ASP MSE PRO MSE GLU ASP PHE CYS LEU GLN SEQRES 26 B 375 LEU LEU GLN GLU HIS GLY VAL LEU LEU VAL PRO GLY ASN SEQRES 27 B 375 ARG PHE GLU ARG ASP GLY TYR VAL ARG LEU GLY PHE ALA SEQRES 28 B 375 CYS GLU GLN GLU THR LEU ILE LYS GLY LEU GLU LYS LEU SEQRES 29 B 375 SER GLN PHE LEU ARG ARG PHE ASP LYS GLU ASN MODRES 3P6K MSE A 156 MET SELENOMETHIONINE MODRES 3P6K MSE A 170 MET SELENOMETHIONINE MODRES 3P6K LLP A 221 LYS MODRES 3P6K MSE A 251 MET SELENOMETHIONINE MODRES 3P6K MSE A 316 MET SELENOMETHIONINE MODRES 3P6K MSE A 318 MET SELENOMETHIONINE MODRES 3P6K MSE B 1 MET SELENOMETHIONINE MODRES 3P6K MSE B 156 MET SELENOMETHIONINE MODRES 3P6K MSE B 170 MET SELENOMETHIONINE MODRES 3P6K LLP B 221 LYS MODRES 3P6K MSE B 251 MET SELENOMETHIONINE MODRES 3P6K MSE B 316 MET SELENOMETHIONINE MODRES 3P6K MSE B 318 MET SELENOMETHIONINE HET MSE A 156 8 HET MSE A 170 8 HET LLP A 221 24 HET MSE A 251 8 HET MSE A 316 8 HET MSE A 318 8 HET MSE B 1 8 HET MSE B 156 8 HET MSE B 170 8 HET LLP B 221 24 HET MSE B 251 8 HET MSE B 316 8 HET MSE B 318 8 HET SO4 A 401 5 HET EDO A 403 4 HET UNL B 390 12 HET UNL B 375 12 HET SO4 B 400 5 HET SO4 B 402 5 HETNAM MSE SELENOMETHIONINE HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM UNL UNKNOWN LIGAND HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 11(C5 H11 N O2 SE) FORMUL 1 LLP 2(C14 H22 N3 O7 P) FORMUL 3 SO4 3(O4 S 2-) FORMUL 4 EDO C2 H6 O2 FORMUL 9 HOH *305(H2 O) HELIX 1 1 PHE A 6 GLU A 16 1 11 HELIX 2 2 ASN A 17 ALA A 19 5 3 HELIX 3 3 THR A 32 GLY A 41 1 10 HELIX 4 4 ASN A 43 GLY A 53 1 11 HELIX 5 5 SER A 64 LEU A 74 1 11 HELIX 6 6 LYS A 79 GLU A 81 5 3 HELIX 7 7 ASN A 87 ILE A 101 1 15 HELIX 8 8 GLN A 115 LEU A 124 1 10 HELIX 9 9 GLU A 134 GLY A 138 5 5 HELIX 10 10 ASP A 142 ILE A 150 1 9 HELIX 11 11 ASP A 171 VAL A 185 1 15 HELIX 12 12 SER A 205 TYR A 210 1 6 HELIX 13 13 LEU A 225 ARG A 229 5 5 HELIX 14 14 ASN A 236 ARG A 244 1 9 HELIX 15 15 TYR A 246 MSE A 251 1 6 HELIX 16 16 GLY A 255 HIS A 268 1 14 HELIX 17 17 HIS A 268 GLU A 294 1 27 HELIX 18 18 PRO A 317 GLY A 330 1 14 HELIX 19 19 ASN A 337 GLU A 340 5 4 HELIX 20 20 GLU A 352 ARG A 368 1 17 HELIX 21 21 ARG A 369 ASP A 371 5 3 HELIX 22 22 PHE B 6 GLU B 16 1 11 HELIX 23 23 ASN B 17 ALA B 19 5 3 HELIX 24 24 THR B 32 GLY B 41 1 10 HELIX 25 25 ASN B 43 GLY B 53 1 11 HELIX 26 26 SER B 64 GLN B 73 1 10 HELIX 27 27 LYS B 79 GLU B 81 5 3 HELIX 28 28 ASN B 87 ILE B 101 1 15 HELIX 29 29 GLN B 115 LEU B 124 1 10 HELIX 30 30 GLU B 134 GLY B 138 5 5 HELIX 31 31 ASP B 142 ILE B 150 1 9 HELIX 32 32 ASP B 171 VAL B 185 1 15 HELIX 33 33 SER B 205 TYR B 210 1 6 HELIX 34 34 LEU B 225 ARG B 229 5 5 HELIX 35 35 ASN B 236 ASP B 245 1 10 HELIX 36 36 GLY B 255 HIS B 268 1 14 HELIX 37 37 HIS B 268 GLU B 294 1 27 HELIX 38 38 PRO B 317 GLY B 330 1 14 HELIX 39 39 ASN B 337 GLU B 340 5 4 HELIX 40 40 GLU B 352 ARG B 368 1 17 HELIX 41 41 ARG B 369 ASP B 371 5 3 SHEET 1 A 2 TYR A 21 ASP A 22 0 SHEET 2 A 2 VAL A 331 LEU A 332 1 O LEU A 332 N TYR A 21 SHEET 1 B 7 ILE A 83 THR A 86 0 SHEET 2 B 7 GLY A 231 ALA A 234 -1 O GLY A 231 N THR A 86 SHEET 3 B 7 GLY A 213 SER A 218 -1 N ALA A 215 O ALA A 234 SHEET 4 B 7 TYR A 188 ASP A 192 1 N SER A 191 O ILE A 214 SHEET 5 B 7 MSE A 156 ASN A 160 1 N ILE A 159 O LEU A 190 SHEET 6 B 7 HIS A 106 TYR A 111 1 N LEU A 110 O CYS A 158 SHEET 7 B 7 GLU A 127 GLN A 132 1 O TRP A 131 N SER A 109 SHEET 1 C 4 VAL A 297 TYR A 299 0 SHEET 2 C 4 SER A 308 ILE A 312 -1 O LYS A 311 N SER A 298 SHEET 3 C 4 TYR A 344 LEU A 347 -1 O LEU A 347 N SER A 308 SHEET 4 C 4 VAL A 334 PRO A 335 -1 N VAL A 334 O ARG A 346 SHEET 1 D 2 TYR B 21 ASP B 22 0 SHEET 2 D 2 VAL B 331 LEU B 332 1 O LEU B 332 N TYR B 21 SHEET 1 E 7 ILE B 83 THR B 86 0 SHEET 2 E 7 GLY B 231 ALA B 234 -1 O GLY B 231 N THR B 86 SHEET 3 E 7 GLY B 213 SER B 218 -1 N ALA B 215 O ALA B 234 SHEET 4 E 7 TYR B 188 ASP B 192 1 N ILE B 189 O ILE B 214 SHEET 5 E 7 THR B 154 ASN B 160 1 N LYS B 155 O TYR B 188 SHEET 6 E 7 HIS B 106 TYR B 111 1 N ILE B 108 O CYS B 158 SHEET 7 E 7 GLU B 127 GLN B 132 1 O TRP B 131 N SER B 109 SHEET 1 F 4 VAL B 297 TYR B 299 0 SHEET 2 F 4 THR B 307 ILE B 312 -1 O LYS B 311 N SER B 298 SHEET 3 F 4 TYR B 344 GLY B 348 -1 O VAL B 345 N VAL B 310 SHEET 4 F 4 VAL B 334 PRO B 335 -1 N VAL B 334 O ARG B 346 LINK C LYS A 155 N MSE A 156 1555 1555 1.34 LINK C MSE A 156 N ILE A 157 1555 1555 1.33 LINK C VAL A 169 N MSE A 170 1555 1555 1.33 LINK C MSE A 170 N ASP A 171 1555 1555 1.32 LINK C LLP A 221 N THR A 222 1555 1555 1.32 LINK C THR A 250 N MSE A 251 1555 1555 1.34 LINK C MSE A 251 N ILE A 252 1555 1555 1.35 LINK C ASP A 315 N MSE A 316 1555 1555 1.33 LINK C MSE A 316 N PRO A 317 1555 1555 1.36 LINK C PRO A 317 N MSE A 318 1555 1555 1.33 LINK C MSE A 318 N GLU A 319 1555 1555 1.34 LINK C MSE B 1 N LYS B 2 1555 1555 1.34 LINK C LYS B 155 N MSE B 156 1555 1555 1.34 LINK C MSE B 156 N ILE B 157 1555 1555 1.34 LINK C VAL B 169 N MSE B 170 1555 1555 1.33 LINK C MSE B 170 N ASP B 171 1555 1555 1.33 LINK C LLP B 221 N THR B 222 1555 1555 1.33 LINK C THR B 250 N MSE B 251 1555 1555 1.33 LINK C MSE B 251 N ILE B 252 1555 1555 1.34 LINK C ASP B 315 N MSE B 316 1555 1555 1.33 LINK C MSE B 316 N PRO B 317 1555 1555 1.35 LINK C PRO B 317 N MSE B 318 1555 1555 1.33 LINK C MSE B 318 N GLU B 319 1555 1555 1.33 CISPEP 1 TYR A 111 PRO A 112 0 -4.67 CISPEP 2 ASN A 161 ALA A 162 0 -2.25 CISPEP 3 ASN A 164 PRO A 165 0 8.04 CISPEP 4 TYR B 111 PRO B 112 0 -4.44 CISPEP 5 ASN B 161 ALA B 162 0 0.41 CISPEP 6 ASN B 164 PRO B 165 0 9.16 SITE 1 AC1 3 SER A 30 LYS B 55 ASN B 57 SITE 1 AC2 4 TRP A 60 HOH A 486 HOH A 513 HOH B 622 SITE 1 AC3 7 LYS A 55 ASN A 57 HOH A 665 SER B 27 SITE 2 AC3 7 ILE B 28 SER B 29 SER B 30 SITE 1 AC4 5 LYS B 55 HIS B 329 GLN B 365 PHE B 366 SITE 2 AC4 5 ARG B 369 CRYST1 83.979 83.979 176.391 90.00 90.00 120.00 P 32 2 1 12 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 0.011908 0.006875 0.000000 0.00000 SCALE2 0.000000 0.013750 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005669 0.00000