HEADER HYDROLASE 27-APR-10 3MQ3 TITLE CRYSTAL STRUCTURE OF NATIVE BOVINE PDP1C COMPND MOL_ID: 1; COMPND 2 MOLECULE: PYRUVATE DEHYDROGENASE PHOSPHATASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDP1C, UNP RESIDUES 72-538; COMPND 5 SYNONYM: PDP 1, PYRUVATE DEHYDROGENASE PHOSPHATASE CATALYTIC SUBUNIT COMPND 6 1, PDPC 1, PROTEIN PHOSPHATASE 2C; COMPND 7 EC: 3.1.3.43; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 GENE: PDP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM 101; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PKK233-3 KEYWDS PHOSPHATASE, PDP1C, PYRUVATE DEHYDROGENASE PHOSPHATASE 1, PYRUVATE KEYWDS 2 DEHYDROGENASE COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.GUO,S.R.ERNST,D.W.CARROLL,M.L.HACKERT REVDAT 3 21-FEB-24 3MQ3 1 REMARK LINK REVDAT 2 08-NOV-17 3MQ3 1 AUTHOR REMARK REVDAT 1 18-MAY-11 3MQ3 0 JRNL AUTH Y.GUO,S.R.ERNST,D.W.CARROLL,M.L.HACKERT JRNL TITL CRYSTAL STRUCTURE OF CATALYTIC SUBUNIT OF BOVINE PYRUVATE JRNL TITL 2 DEHYDROGENASE PHOPHATASE JRNL REF TO BE PUBLISHED 2010 JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 13413 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) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 716 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) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 959 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.08 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 65 REMARK 3 BIN FREE R VALUE : 0.3690 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2967 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 99 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.60000 REMARK 3 B22 (A**2) : 0.60000 REMARK 3 B33 (A**2) : -0.90000 REMARK 3 B12 (A**2) : 0.30000 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): 1.094 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.393 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.270 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.486 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.909 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.863 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3036 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4125 ; 1.894 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 372 ; 7.782 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 150 ;38.326 ;24.067 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 484 ;18.623 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;20.781 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 461 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2338 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1492 ; 0.257 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2046 ; 0.320 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 172 ; 0.202 ; 0.200 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): 27 ; 0.197 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.142 ; 0.200 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): 1931 ; 1.106 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3020 ; 1.832 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1249 ; 2.478 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1105 ; 3.701 ; 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 3MQ3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058858. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 1.5418 REMARK 200 MONOCHROMATOR : BLUE MAX-FLUX OPTICAL SYSTEM REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14135 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 27.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.34000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB: REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.68 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE PROTEIN SOLUTION WAS 20MG/ML IN 10 REMARK 280 MM TRIS-HCL, PH 7.3, 50 MM NACL, 1MM MNSO4, 2MM DTT, AND 1MM REMARK 280 BENZAMIDE. THE WELL SOLUTION (MIXED 1:1) CONTAINED 0.10M HEPES, REMARK 280 PH 7.5 AND 20% JEFFAMINE M-600., HANGING DROP, TEMPERATURE 298K 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 115.09133 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 57.54567 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 57.54567 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 115.09133 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: BIOLOGICAL UNIT IS THE SAME AS ASYM. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ALA A 1 REMARK 465 SER A 2 REMARK 465 THR A 3 REMARK 465 PRO A 4 REMARK 465 GLN A 5 REMARK 465 LYS A 6 REMARK 465 PHE A 7 REMARK 465 TYR A 8 REMARK 465 LEU A 9 REMARK 465 THR A 10 REMARK 465 VAL A 109 REMARK 465 GLU A 110 REMARK 465 SER A 111 REMARK 465 GLY A 112 REMARK 465 ARG A 113 REMARK 465 ALA A 114 REMARK 465 LEU A 151 REMARK 465 ASN A 152 REMARK 465 THR A 153 REMARK 465 GLY A 154 REMARK 465 GLU A 155 REMARK 465 SER A 156 REMARK 465 THR A 157 REMARK 465 ASP A 158 REMARK 465 SER A 300 REMARK 465 GLY A 301 REMARK 465 PRO A 302 REMARK 465 ASP A 303 REMARK 465 GLN A 304 REMARK 465 LEU A 305 REMARK 465 ASN A 306 REMARK 465 ASP A 307 REMARK 465 ASN A 308 REMARK 465 GLU A 309 REMARK 465 TYR A 310 REMARK 465 THR A 311 REMARK 465 HIS A 370 REMARK 465 HIS A 371 REMARK 465 GLN A 372 REMARK 465 GLN A 373 REMARK 465 PRO A 374 REMARK 465 ILE A 375 REMARK 465 ALA A 376 REMARK 465 VAL A 377 REMARK 465 GLY A 378 REMARK 465 GLY A 379 REMARK 465 TYR A 380 REMARK 465 LYS A 381 REMARK 465 VAL A 382 REMARK 465 THR A 383 REMARK 465 LEU A 384 REMARK 465 GLY A 385 REMARK 465 GLN A 386 REMARK 465 MET A 387 REMARK 465 HIS A 388 REMARK 465 GLY A 389 REMARK 465 LEU A 390 REMARK 465 LEU A 391 REMARK 465 THR A 392 REMARK 465 GLU A 393 REMARK 465 ARG A 394 REMARK 465 ARG A 395 REMARK 465 ALA A 396 REMARK 465 LYS A 397 REMARK 465 MET A 398 REMARK 465 SER A 399 REMARK 465 SER A 400 REMARK 465 VAL A 401 REMARK 465 PHE A 402 REMARK 465 GLU A 403 REMARK 465 ASP A 404 REMARK 465 GLY A 417 REMARK 465 ASN A 418 REMARK 465 ASN A 419 REMARK 465 GLU A 420 REMARK 465 PHE A 421 REMARK 465 GLY A 422 REMARK 465 ALA A 423 REMARK 465 VAL A 424 REMARK 465 ASP A 425 REMARK 465 HIS A 426 REMARK 465 GLU A 427 REMARK 465 ARG A 428 REMARK 465 LEU A 429 REMARK 465 SER A 430 REMARK 465 ASN A 464 REMARK 465 GLN A 465 REMARK 465 GLU A 466 REMARK 465 GLN A 467 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 13 CG CD OE1 NE2 REMARK 470 VAL A 14 CG1 CG2 REMARK 470 SER A 16 OG REMARK 470 LYS A 19 CG CD CE NZ REMARK 470 LYS A 131 CG CD CE NZ REMARK 470 LYS A 135 CG CD CE NZ REMARK 470 ILE A 159 CG1 CG2 CD1 REMARK 470 GLN A 246 CG CD OE1 NE2 REMARK 470 LYS A 260 CG CD CE NZ REMARK 470 LYS A 312 CG CD CE NZ REMARK 470 PHE A 313 CG CD1 CD2 CE1 CE2 CZ REMARK 470 THR A 331 OG1 CG2 REMARK 470 MET A 369 CG SD CE REMARK 470 GLU A 437 CG CD OE1 OE2 REMARK 470 LEU A 439 CG CD1 CD2 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 253 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 PRO A 315 C - N - CD ANGL. DEV. = -17.5 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 GLN A 13 19.74 142.52 REMARK 500 SER A 24 130.35 173.06 REMARK 500 ALA A 50 -98.57 -43.77 REMARK 500 ASN A 107 -79.73 -56.33 REMARK 500 LEU A 275 -71.50 -114.84 REMARK 500 ILE A 298 82.17 -45.79 REMARK 500 PRO A 316 -149.00 -86.69 REMARK 500 SER A 434 80.33 -66.71 REMARK 500 LEU A 435 -51.99 -135.58 REMARK 500 GLU A 437 178.36 84.90 REMARK 500 GLU A 438 28.43 -79.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA A 50 PRO A 51 145.77 REMARK 500 LYS A 312 PHE A 313 -140.40 REMARK 500 ASN A 317 TYR A 318 -131.43 REMARK 500 LEU A 435 PRO A 436 -147.69 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 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 73 OD2 REMARK 620 2 GLY A 74 O 82.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 502 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 73 OD1 REMARK 620 2 ASP A 347 OD1 92.8 REMARK 620 3 ASP A 445 OD2 177.7 89.4 REMARK 620 4 HOH A 504 O 90.5 84.8 90.1 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 MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3N3C RELATED DB: PDB DBREF 3MQ3 A 1 467 UNP P35816 PDP1_BOVIN 72 538 SEQRES 1 A 467 ALA SER THR PRO GLN LYS PHE TYR LEU THR PRO PRO GLN SEQRES 2 A 467 VAL ASN SER ILE LEU LYS ALA ASN GLU TYR SER PHE LYS SEQRES 3 A 467 VAL PRO GLU PHE ASP GLY LYS ASN VAL SER SER VAL LEU SEQRES 4 A 467 GLY PHE ASP SER ASN GLN LEU PRO ALA ASN ALA PRO ILE SEQRES 5 A 467 GLU ASP ARG ARG SER ALA ALA THR CYS LEU GLN THR ARG SEQRES 6 A 467 GLY MET LEU LEU GLY VAL PHE ASP GLY HIS ALA GLY CYS SEQRES 7 A 467 ALA CYS SER GLN ALA VAL SER GLU ARG LEU PHE TYR TYR SEQRES 8 A 467 ILE ALA VAL SER LEU LEU PRO HIS GLU THR LEU LEU GLU SEQRES 9 A 467 ILE GLU ASN ALA VAL GLU SER GLY ARG ALA LEU LEU PRO SEQRES 10 A 467 ILE LEU GLN TRP HIS LYS HIS PRO ASN ASP TYR PHE SER SEQRES 11 A 467 LYS GLU ALA SER LYS LEU TYR PHE ASN SER LEU ARG THR SEQRES 12 A 467 TYR TRP GLN GLU LEU ILE ASP LEU ASN THR GLY GLU SER SEQRES 13 A 467 THR ASP ILE ASP VAL LYS GLU ALA LEU ILE ASN ALA PHE SEQRES 14 A 467 LYS ARG LEU ASP ASN ASP ILE SER LEU GLU ALA GLN VAL SEQRES 15 A 467 GLY ASP PRO ASN SER PHE LEU ASN TYR LEU VAL LEU ARG SEQRES 16 A 467 VAL ALA PHE SER GLY ALA THR ALA CYS VAL ALA HIS VAL SEQRES 17 A 467 ASP GLY VAL ASP LEU HIS VAL ALA ASN THR GLY ASP SER SEQRES 18 A 467 ARG ALA MET LEU GLY VAL GLN GLU GLU ASP GLY SER TRP SEQRES 19 A 467 SER ALA VAL THR LEU SER ASN ASP HIS ASN ALA GLN ASN SEQRES 20 A 467 GLU ARG GLU VAL GLU ARG LEU LYS LEU GLU HIS PRO LYS SEQRES 21 A 467 ASN GLU ALA LYS SER VAL VAL LYS GLN ASP ARG LEU LEU SEQRES 22 A 467 GLY LEU LEU MET PRO PHE ARG ALA PHE GLY ASP VAL LYS SEQRES 23 A 467 PHE LYS TRP SER ILE ASP LEU GLN LYS ARG VAL ILE GLU SEQRES 24 A 467 SER GLY PRO ASP GLN LEU ASN ASP ASN GLU TYR THR LYS SEQRES 25 A 467 PHE ILE PRO PRO ASN TYR TYR THR PRO PRO TYR LEU THR SEQRES 26 A 467 ALA GLU PRO GLU VAL THR TYR HIS ARG LEU ARG PRO GLN SEQRES 27 A 467 ASP LYS PHE LEU VAL LEU ALA THR ASP GLY LEU TRP GLU SEQRES 28 A 467 THR MET HIS ARG GLN ASP VAL VAL ARG ILE VAL GLY GLU SEQRES 29 A 467 TYR LEU THR GLY MET HIS HIS GLN GLN PRO ILE ALA VAL SEQRES 30 A 467 GLY GLY TYR LYS VAL THR LEU GLY GLN MET HIS GLY LEU SEQRES 31 A 467 LEU THR GLU ARG ARG ALA LYS MET SER SER VAL PHE GLU SEQRES 32 A 467 ASP GLN ASN ALA ALA THR HIS LEU ILE ARG HIS ALA VAL SEQRES 33 A 467 GLY ASN ASN GLU PHE GLY ALA VAL ASP HIS GLU ARG LEU SEQRES 34 A 467 SER LYS MET LEU SER LEU PRO GLU GLU LEU ALA ARG MET SEQRES 35 A 467 TYR ARG ASP ASP ILE THR ILE ILE VAL VAL GLN PHE ASN SEQRES 36 A 467 SER HIS VAL VAL GLY ALA TYR GLN ASN GLN GLU GLN HET MN A 501 1 HET MN A 502 1 HETNAM MN MANGANESE (II) ION FORMUL 2 MN 2(MN 2+) FORMUL 4 HOH *99(H2 O) HELIX 1 1 GLN A 13 LYS A 19 1 7 HELIX 2 2 CYS A 78 SER A 95 1 18 HELIX 3 3 PRO A 98 ALA A 108 1 11 HELIX 4 4 ALA A 133 ASP A 150 1 18 HELIX 5 5 ASP A 160 GLY A 183 1 24 HELIX 6 6 ASN A 186 SER A 199 1 14 HELIX 7 7 ASN A 247 LEU A 256 1 10 HELIX 8 8 GLU A 257 HIS A 258 5 2 HELIX 9 9 PRO A 259 ALA A 263 5 5 HELIX 10 10 VAL A 285 LYS A 288 5 4 HELIX 11 11 SER A 290 ILE A 298 1 9 HELIX 12 12 THR A 346 GLU A 351 1 6 HELIX 13 13 HIS A 354 THR A 367 1 14 HELIX 14 14 ASN A 406 VAL A 416 1 11 HELIX 15 15 LEU A 439 TYR A 443 5 5 HELIX 16 16 ASN A 455 TYR A 462 1 8 SHEET 1 A 6 TYR A 23 LYS A 26 0 SHEET 2 A 6 VAL A 38 LEU A 46 -1 O SER A 43 N TYR A 23 SHEET 3 A 6 ILE A 447 PHE A 454 -1 O GLN A 453 N GLY A 40 SHEET 4 A 6 ASP A 339 ALA A 345 -1 N LEU A 344 O ILE A 450 SHEET 5 A 6 ARG A 222 GLN A 228 -1 N MET A 224 O VAL A 343 SHEET 6 A 6 TRP A 234 THR A 238 -1 O SER A 235 N VAL A 227 SHEET 1 B 5 LEU A 119 TRP A 121 0 SHEET 2 B 5 ASP A 54 CYS A 61 -1 N THR A 60 O GLN A 120 SHEET 3 B 5 MET A 67 HIS A 75 -1 O LEU A 68 N ALA A 59 SHEET 4 B 5 GLY A 200 ALA A 201 -1 O GLY A 200 N HIS A 75 SHEET 5 B 5 PHE A 282 GLY A 283 -1 O PHE A 282 N ALA A 201 SHEET 1 C 6 LEU A 119 TRP A 121 0 SHEET 2 C 6 ASP A 54 CYS A 61 -1 N THR A 60 O GLN A 120 SHEET 3 C 6 MET A 67 HIS A 75 -1 O LEU A 68 N ALA A 59 SHEET 4 C 6 ALA A 203 ASP A 209 -1 O ALA A 206 N LEU A 69 SHEET 5 C 6 ASP A 212 THR A 218 -1 O THR A 218 N ALA A 203 SHEET 6 C 6 GLU A 329 ARG A 334 -1 O GLU A 329 N ASN A 217 SHEET 1 D 2 VAL A 267 LYS A 268 0 SHEET 2 D 2 ARG A 271 LEU A 272 -1 O ARG A 271 N LYS A 268 LINK OD2 ASP A 73 MN MN A 501 1555 1555 2.01 LINK OD1 ASP A 73 MN MN A 502 1555 1555 2.19 LINK O GLY A 74 MN MN A 501 1555 1555 2.21 LINK OD1 ASP A 347 MN MN A 502 1555 1555 2.14 LINK OD2 ASP A 445 MN MN A 502 1555 1555 2.18 LINK MN MN A 502 O HOH A 504 1555 1555 1.95 CISPEP 1 PRO A 321 PRO A 322 0 10.40 SITE 1 AC1 3 ASP A 73 GLY A 74 GLU A 230 SITE 1 AC2 5 ASP A 73 GLU A 230 ASP A 347 ASP A 445 SITE 2 AC2 5 HOH A 504 CRYST1 75.274 75.274 172.637 90.00 90.00 120.00 P 32 2 1 6 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 0.013285 0.007670 0.000000 0.00000 SCALE2 0.000000 0.015340 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005793 0.00000