HEADER TRANSFERASE 29-OCT-09 3KGX TITLE CRYSTAL STRUCTURE OF PUTATIVE AMINOTRANSFERASE (AAH25799.1) FROM MUS TITLE 2 MUSCULUS AT 1.80 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALANINE-GLYOXYLATE AMINOTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALANINE-GLYOXYLATE AMINOTRANSFERASE ISOFORM CRA_B; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: AAH25799.1, AGXT, MCG_16569; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: HEK293; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PRSPEEDET KEYWDS PUTATIVE AMINOTRANSFERASE, STRUCTURAL GENOMICS, JOINT CENTER FOR KEYWDS 2 STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, KEYWDS 3 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 6 20-SEP-23 3KGX 1 REMARK REVDAT 5 01-FEB-23 3KGX 1 REMARK SEQADV REVDAT 4 17-JUL-19 3KGX 1 REMARK REVDAT 3 01-NOV-17 3KGX 1 REMARK REVDAT 2 13-JUL-11 3KGX 1 VERSN REVDAT 1 10-NOV-09 3KGX 0 JRNL AUTH JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) JRNL TITL CRYSTAL STRUCTURE OF PUTATIVE AMINOTRANSFERASE (AAH25799.1) JRNL TITL 2 FROM MUS MUSCULUS AT 1.80 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 76018 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3820 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5309 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE SET COUNT : 270 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5953 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 502 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 22.06 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.23000 REMARK 3 B22 (A**2) : -0.91000 REMARK 3 B33 (A**2) : 1.14000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.122 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.116 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.770 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6385 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4385 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8721 ; 1.832 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10762 ; 1.350 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 853 ; 3.981 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 261 ;32.872 ;23.372 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1095 ;11.040 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 45 ;13.417 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1000 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7121 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1252 ; 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): 3988 ; 0.723 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1611 ; 0.183 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6488 ; 1.326 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2397 ; 2.038 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2194 ; 3.298 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 27 A 277 REMARK 3 RESIDUE RANGE : A 281 A 412 REMARK 3 ORIGIN FOR THE GROUP (A): 1.5370 12.0460 5.2390 REMARK 3 T TENSOR REMARK 3 T11: 0.0432 T22: 0.0719 REMARK 3 T33: 0.0130 T12: 0.0036 REMARK 3 T13: 0.0107 T23: -0.0045 REMARK 3 L TENSOR REMARK 3 L11: 0.9488 L22: 0.8571 REMARK 3 L33: 0.4967 L12: 0.1597 REMARK 3 L13: 0.2052 L23: 0.1442 REMARK 3 S TENSOR REMARK 3 S11: 0.0507 S12: 0.0719 S13: -0.0371 REMARK 3 S21: 0.0532 S22: -0.0607 S23: 0.0664 REMARK 3 S31: 0.0842 S32: -0.0006 S33: 0.0100 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 23 B 412 REMARK 3 ORIGIN FOR THE GROUP (A): 2.8090 21.3620 33.5800 REMARK 3 T TENSOR REMARK 3 T11: 0.1097 T22: 0.0723 REMARK 3 T33: 0.1254 T12: 0.0009 REMARK 3 T13: -0.0107 T23: -0.0458 REMARK 3 L TENSOR REMARK 3 L11: 0.5448 L22: 0.2532 REMARK 3 L33: 1.4480 L12: -0.1396 REMARK 3 L13: 0.1813 L23: -0.0890 REMARK 3 S TENSOR REMARK 3 S11: -0.1155 S12: -0.0782 S13: 0.0722 REMARK 3 S21: 0.1284 S22: -0.0598 S23: -0.0028 REMARK 3 S31: 0.0766 S32: -0.0862 S33: 0.1753 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 RECORDS CONTAIN RESIDUAL B FACTORS REMARK 3 ONLY. 3. ETHYLENE GLYCOL (EDO) MOLECULES AND CHLORIDE (CL) IONS REMARK 3 FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTION ARE MODELED. REMARK 4 REMARK 4 3KGX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055978. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9765 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.5 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76087 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 29.696 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : 0.08200 REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.68400 REMARK 200 R SYM FOR SHELL (I) : 0.68400 REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MR REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 3KGW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20.0000% POLYETHYLENE GLYCOL 3350, REMARK 280 0.2000M AMMONIUM FLUORIDE, NO BUFFER PH 6.2, NANODROP, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 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 30.69550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.67550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.28250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 58.67550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.69550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.28250 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 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: 10840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 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 MET A 23 REMARK 465 GLY A 24 REMARK 465 SER A 25 REMARK 465 TYR A 26 REMARK 465 GLU A 278 REMARK 465 THR A 279 REMARK 465 ARG A 280 REMARK 465 LYS A 413 REMARK 465 LEU A 414 REMARK 465 GLY B 0 REMARK 465 LYS B 413 REMARK 465 LEU B 414 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 GLN A 27 CG CD OE1 NE2 REMARK 470 GLU A 34 CG CD OE1 OE2 REMARK 470 LYS A 38 CG CD CE NZ REMARK 470 MET A 71 CG SD CE REMARK 470 LYS A 73 CE NZ REMARK 470 LYS A 258 CE NZ REMARK 470 ILE A 282 CG1 CG2 CD1 REMARK 470 HIS A 284 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 325 CD OE1 NE2 REMARK 470 MET B 71 CG SD CE REMARK 470 LYS B 73 CG CD CE NZ REMARK 470 GLU B 193 CD OE1 OE2 REMARK 470 GLN B 230 CG CD OE1 NE2 REMARK 470 LYS B 247 CD CE NZ REMARK 470 LYS B 256 CE NZ REMARK 470 ARG B 280 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 283 CG ND1 CD2 CE1 NE2 REMARK 470 THR B 285 OG1 CG2 REMARK 470 SER B 290 OG REMARK 470 GLU B 307 CD OE1 OE2 REMARK 470 ARG B 311 CZ NH1 NH2 REMARK 470 LYS B 334 CD CE NZ 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 CYS B 106 CB CYS B 106 SG -0.111 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 PRO B 237 C - N - CA ANGL. DEV. = 43.4 DEGREES REMARK 500 PRO B 237 C - N - CD ANGL. DEV. = -44.3 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 LYS A 231 -115.15 -100.24 REMARK 500 THR A 285 68.00 -103.78 REMARK 500 GLU A 378 -3.49 71.05 REMARK 500 LYS B 231 -115.09 -104.23 REMARK 500 PRO B 236 -131.10 -19.61 REMARK 500 PRO B 237 114.35 23.32 REMARK 500 HIS B 284 -103.69 51.63 REMARK 500 GLU B 378 -4.77 71.68 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 MG A 503 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 319 NE2 REMARK 620 2 HIS A 323 NE2 95.6 REMARK 620 3 ASP A 396 OD1 90.6 100.3 REMARK 620 4 HOH A 679 O 136.2 101.3 124.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 511 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 512 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 402064 RELATED DB: TARGETDB REMARK 900 RELATED ID: 3KGW RELATED DB: PDB REMARK 900 THE SAME PROTEIN WITH PARTIALLY OCCUPIED ENDOGENOUS PYRIDOXAL-5'- REMARK 900 PHOSPHATE BOUND REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS CONSTRUCT (RESIDUE 23-414) WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. DBREF 3KGX A 23 414 UNP Q8R128 Q8R128_MOUSE 23 414 DBREF 3KGX B 23 414 UNP Q8R128 Q8R128_MOUSE 23 414 SEQADV 3KGX GLY A 0 UNP Q8R128 EXPRESSION TAG SEQADV 3KGX GLY B 0 UNP Q8R128 EXPRESSION TAG SEQRES 1 A 393 GLY MET GLY SER TYR GLN LEU LEU VAL PRO PRO PRO GLU SEQRES 2 A 393 ALA LEU SER LYS PRO LEU SER VAL PRO THR ARG LEU LEU SEQRES 3 A 393 LEU GLY PRO GLY PRO SER ASN LEU ALA PRO ARG VAL LEU SEQRES 4 A 393 ALA ALA GLY SER LEU ARG MET ILE GLY HIS MET GLN LYS SEQRES 5 A 393 GLU MET LEU GLN ILE MET GLU GLU ILE LYS GLN GLY ILE SEQRES 6 A 393 GLN TYR VAL PHE GLN THR ARG ASN PRO LEU THR LEU VAL SEQRES 7 A 393 VAL SER GLY SER GLY HIS CYS ALA MET GLU THR ALA LEU SEQRES 8 A 393 PHE ASN LEU LEU GLU PRO GLY ASP SER PHE LEU THR GLY SEQRES 9 A 393 THR ASN GLY ILE TRP GLY MET ARG ALA ALA GLU ILE ALA SEQRES 10 A 393 ASP ARG ILE GLY ALA ARG VAL HIS GLN MET ILE LYS LYS SEQRES 11 A 393 PRO GLY GLU HIS TYR THR LEU GLN GLU VAL GLU GLU GLY SEQRES 12 A 393 LEU ALA GLN HIS LYS PRO VAL LEU LEU PHE LEU VAL HIS SEQRES 13 A 393 GLY GLU SER SER THR GLY VAL VAL GLN PRO LEU ASP GLY SEQRES 14 A 393 PHE GLY GLU LEU CYS HIS ARG TYR GLN CYS LEU LEU LEU SEQRES 15 A 393 VAL ASP SER VAL ALA SER LEU GLY GLY VAL PRO ILE TYR SEQRES 16 A 393 MET ASP GLN GLN GLY ILE ASP ILE MET TYR SER SER SER SEQRES 17 A 393 GLN LYS VAL LEU ASN ALA PRO PRO GLY ILE SER LEU ILE SEQRES 18 A 393 SER PHE ASN ASP LYS ALA LYS TYR LYS VAL TYR SER ARG SEQRES 19 A 393 LYS THR LYS PRO VAL SER PHE TYR THR ASP ILE THR TYR SEQRES 20 A 393 LEU ALA LYS LEU TRP GLY CYS GLU GLY GLU THR ARG VAL SEQRES 21 A 393 ILE HIS HIS THR THR PRO VAL THR SER LEU TYR CYS LEU SEQRES 22 A 393 ARG GLU SER LEU ALA LEU ILE ALA GLU GLN GLY LEU GLU SEQRES 23 A 393 ASN CYS TRP ARG ARG HIS ARG GLU ALA THR ALA HIS LEU SEQRES 24 A 393 HIS LYS HIS LEU GLN GLU MET GLY LEU LYS PHE PHE VAL SEQRES 25 A 393 LYS ASP PRO GLU ILE ARG LEU PRO THR ILE THR THR VAL SEQRES 26 A 393 THR VAL PRO ALA GLY TYR ASN TRP ARG ASP ILE VAL SER SEQRES 27 A 393 TYR VAL LEU ASP HIS PHE SER ILE GLU ILE SER GLY GLY SEQRES 28 A 393 LEU GLY PRO THR GLU GLU ARG VAL LEU ARG ILE GLY LEU SEQRES 29 A 393 LEU GLY TYR ASN ALA THR THR GLU ASN VAL ASP ARG VAL SEQRES 30 A 393 ALA GLU ALA LEU ARG GLU ALA LEU GLN HIS CYS PRO LYS SEQRES 31 A 393 ASN LYS LEU SEQRES 1 B 393 GLY MET GLY SER TYR GLN LEU LEU VAL PRO PRO PRO GLU SEQRES 2 B 393 ALA LEU SER LYS PRO LEU SER VAL PRO THR ARG LEU LEU SEQRES 3 B 393 LEU GLY PRO GLY PRO SER ASN LEU ALA PRO ARG VAL LEU SEQRES 4 B 393 ALA ALA GLY SER LEU ARG MET ILE GLY HIS MET GLN LYS SEQRES 5 B 393 GLU MET LEU GLN ILE MET GLU GLU ILE LYS GLN GLY ILE SEQRES 6 B 393 GLN TYR VAL PHE GLN THR ARG ASN PRO LEU THR LEU VAL SEQRES 7 B 393 VAL SER GLY SER GLY HIS CYS ALA MET GLU THR ALA LEU SEQRES 8 B 393 PHE ASN LEU LEU GLU PRO GLY ASP SER PHE LEU THR GLY SEQRES 9 B 393 THR ASN GLY ILE TRP GLY MET ARG ALA ALA GLU ILE ALA SEQRES 10 B 393 ASP ARG ILE GLY ALA ARG VAL HIS GLN MET ILE LYS LYS SEQRES 11 B 393 PRO GLY GLU HIS TYR THR LEU GLN GLU VAL GLU GLU GLY SEQRES 12 B 393 LEU ALA GLN HIS LYS PRO VAL LEU LEU PHE LEU VAL HIS SEQRES 13 B 393 GLY GLU SER SER THR GLY VAL VAL GLN PRO LEU ASP GLY SEQRES 14 B 393 PHE GLY GLU LEU CYS HIS ARG TYR GLN CYS LEU LEU LEU SEQRES 15 B 393 VAL ASP SER VAL ALA SER LEU GLY GLY VAL PRO ILE TYR SEQRES 16 B 393 MET ASP GLN GLN GLY ILE ASP ILE MET TYR SER SER SER SEQRES 17 B 393 GLN LYS VAL LEU ASN ALA PRO PRO GLY ILE SER LEU ILE SEQRES 18 B 393 SER PHE ASN ASP LYS ALA LYS TYR LYS VAL TYR SER ARG SEQRES 19 B 393 LYS THR LYS PRO VAL SER PHE TYR THR ASP ILE THR TYR SEQRES 20 B 393 LEU ALA LYS LEU TRP GLY CYS GLU GLY GLU THR ARG VAL SEQRES 21 B 393 ILE HIS HIS THR THR PRO VAL THR SER LEU TYR CYS LEU SEQRES 22 B 393 ARG GLU SER LEU ALA LEU ILE ALA GLU GLN GLY LEU GLU SEQRES 23 B 393 ASN CYS TRP ARG ARG HIS ARG GLU ALA THR ALA HIS LEU SEQRES 24 B 393 HIS LYS HIS LEU GLN GLU MET GLY LEU LYS PHE PHE VAL SEQRES 25 B 393 LYS ASP PRO GLU ILE ARG LEU PRO THR ILE THR THR VAL SEQRES 26 B 393 THR VAL PRO ALA GLY TYR ASN TRP ARG ASP ILE VAL SER SEQRES 27 B 393 TYR VAL LEU ASP HIS PHE SER ILE GLU ILE SER GLY GLY SEQRES 28 B 393 LEU GLY PRO THR GLU GLU ARG VAL LEU ARG ILE GLY LEU SEQRES 29 B 393 LEU GLY TYR ASN ALA THR THR GLU ASN VAL ASP ARG VAL SEQRES 30 B 393 ALA GLU ALA LEU ARG GLU ALA LEU GLN HIS CYS PRO LYS SEQRES 31 B 393 ASN LYS LEU HET CL A 502 1 HET MG A 503 1 HET EDO A 504 4 HET EDO A 505 4 HET EDO A 507 4 HET EDO A 508 4 HET EDO A 510 4 HET EDO A 511 4 HET CL B 501 1 HET EDO B 506 4 HET EDO B 509 4 HET EDO B 512 4 HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 CL 2(CL 1-) FORMUL 4 MG MG 2+ FORMUL 5 EDO 9(C2 H6 O2) FORMUL 15 HOH *502(H2 O) HELIX 1 1 PRO A 33 LYS A 38 5 6 HELIX 2 2 ALA A 56 GLY A 63 1 8 HELIX 3 3 GLN A 72 GLN A 91 1 20 HELIX 4 4 CYS A 106 LEU A 116 1 11 HELIX 5 5 GLY A 128 ILE A 141 1 14 HELIX 6 6 THR A 157 LYS A 169 1 13 HELIX 7 7 GLY A 190 TYR A 198 1 9 HELIX 8 8 ASN A 245 SER A 254 1 10 HELIX 9 9 ASP A 265 TRP A 273 1 9 HELIX 10 10 PRO A 287 GLY A 305 1 19 HELIX 11 11 GLY A 305 MET A 327 1 23 HELIX 12 12 ASP A 335 ARG A 339 5 5 HELIX 13 13 ASN A 353 SER A 366 1 14 HELIX 14 14 LEU A 373 GLU A 377 5 5 HELIX 15 15 LEU A 386 ALA A 390 5 5 HELIX 16 16 THR A 391 CYS A 409 1 19 HELIX 17 17 PRO B 33 LYS B 38 5 6 HELIX 18 18 ALA B 56 GLY B 63 1 8 HELIX 19 19 GLN B 72 GLN B 91 1 20 HELIX 20 20 CYS B 106 LEU B 116 1 11 HELIX 21 21 GLY B 128 ILE B 141 1 14 HELIX 22 22 THR B 157 LYS B 169 1 13 HELIX 23 23 GLY B 190 TYR B 198 1 9 HELIX 24 24 ASN B 245 SER B 254 1 10 HELIX 25 25 ASP B 265 TRP B 273 1 9 HELIX 26 26 PRO B 287 GLY B 305 1 19 HELIX 27 27 GLY B 305 MET B 327 1 23 HELIX 28 28 ASP B 335 ARG B 339 5 5 HELIX 29 29 ASN B 353 SER B 366 1 14 HELIX 30 30 LEU B 373 GLU B 377 5 5 HELIX 31 31 LEU B 386 ALA B 390 5 5 HELIX 32 32 THR B 391 CYS B 409 1 19 SHEET 1 A 2 LEU A 46 LEU A 47 0 SHEET 2 A 2 ILE A 367 GLU A 368 1 O GLU A 368 N LEU A 46 SHEET 1 B 7 LEU A 96 SER A 101 0 SHEET 2 B 7 ILE A 239 PHE A 244 -1 O SER A 240 N VAL A 100 SHEET 3 B 7 ILE A 224 SER A 228 -1 N SER A 227 O LEU A 241 SHEET 4 B 7 LEU A 201 ASP A 205 1 N VAL A 204 O ILE A 224 SHEET 5 B 7 LEU A 172 VAL A 176 1 N LEU A 173 O LEU A 203 SHEET 6 B 7 SER A 121 THR A 126 1 N LEU A 123 O PHE A 174 SHEET 7 B 7 ARG A 144 ILE A 149 1 O HIS A 146 N PHE A 122 SHEET 1 C 2 GLY A 178 GLU A 179 0 SHEET 2 C 2 VAL A 184 VAL A 185 -1 O VAL A 184 N GLU A 179 SHEET 1 D 2 ILE A 343 THR A 347 0 SHEET 2 D 2 VAL A 380 GLY A 384 -1 O LEU A 381 N VAL A 346 SHEET 1 E 2 LEU B 46 LEU B 47 0 SHEET 2 E 2 ILE B 367 GLU B 368 1 O GLU B 368 N LEU B 46 SHEET 1 F 7 LEU B 96 SER B 101 0 SHEET 2 F 7 ILE B 239 PHE B 244 -1 O SER B 240 N VAL B 100 SHEET 3 F 7 ILE B 224 SER B 228 -1 N SER B 227 O LEU B 241 SHEET 4 F 7 LEU B 201 ASP B 205 1 N VAL B 204 O ILE B 224 SHEET 5 F 7 LEU B 172 VAL B 176 1 N LEU B 173 O LEU B 203 SHEET 6 F 7 SER B 121 THR B 126 1 N LEU B 123 O PHE B 174 SHEET 7 F 7 ARG B 144 ILE B 149 1 O MET B 148 N THR B 124 SHEET 1 G 2 GLY B 178 GLU B 179 0 SHEET 2 G 2 VAL B 184 VAL B 185 -1 O VAL B 184 N GLU B 179 SHEET 1 H 2 ILE B 343 THR B 347 0 SHEET 2 H 2 VAL B 380 GLY B 384 -1 O LEU B 381 N VAL B 346 LINK NE2 HIS A 319 MG MG A 503 1555 1555 2.23 LINK NE2 HIS A 323 MG MG A 503 1555 1555 2.18 LINK OD1 ASP A 396 MG MG A 503 1555 1555 1.76 LINK MG MG A 503 O HOH A 679 1555 1555 1.91 CISPEP 1 GLY A 51 PRO A 52 0 -2.79 CISPEP 2 GLY B 51 PRO B 52 0 -0.86 CISPEP 3 PRO B 236 PRO B 237 0 2.12 CISPEP 4 PRO B 236 PRO B 237 0 14.09 SITE 1 AC1 4 ASN A 54 LEU A 55 HOH A 789 MET B 67 SITE 1 AC2 5 HIS A 319 HIS A 323 ASP A 396 HOH A 678 SITE 2 AC2 5 HOH A 679 SITE 1 AC3 6 GLU A 315 THR A 392 HOH A 700 HOH A 744 SITE 2 AC3 6 ARG B 403 HOH B 740 SITE 1 AC4 8 PHE A 113 LEU A 116 GLU A 117 PRO A 118 SITE 2 AC4 8 ILE A 141 ARG A 255 PRO A 259 VAL A 260 SITE 1 AC5 7 ARG A 93 PRO A 95 VAL A 145 ASP A 246 SITE 2 AC5 7 HOH A 603 HOH A 626 HOH A 813 SITE 1 AC6 6 PRO A 187 LEU A 188 ASP A 189 HOH A 628 SITE 2 AC6 6 HOH A 801 HOH A 820 SITE 1 AC7 3 GLU A 109 GLU B 109 HOH B 665 SITE 1 AC8 4 GLY A 190 HOH A 672 HOH A 681 ARG B 255 SITE 1 AC9 5 ARG A 66 MET A 67 ASN B 54 LEU B 55 SITE 2 AC9 5 HOH B 768 SITE 1 BC1 7 PHE B 113 LEU B 116 GLU B 117 ILE B 141 SITE 2 BC1 7 ARG B 255 PRO B 259 VAL B 260 SITE 1 BC2 3 ILE B 129 ARG B 133 HOH B 671 SITE 1 BC3 5 LEU B 188 ASP B 189 HOH B 620 HOH B 758 SITE 2 BC3 5 HOH B 814 CRYST1 61.391 112.565 117.351 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 0.016289 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008884 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008521 0.00000