HEADER PROTEIN BINDING 30-SEP-15 5E1Y
TITLE PDZ2 OF LNX2 AT 277K, MODEL WITH ALTERNATE CONFORMATIONS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LIGAND OF NUMB PROTEIN X 2;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: SECOND PDZ DOMAIN (UNP RESIDUES 336-424);
COMPND 5 SYNONYM: NUMB-BINDING PROTEIN 2,PDZ DOMAIN-CONTAINING RING FINGER
COMPND 6 PROTEIN 1;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: LNX2, PDZRN1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC28
KEYWDS ROOM TEMPERATURE, PROTEIN BINDING
EXPDTA X-RAY DIFFRACTION
AUTHOR D.R.HEKSTRA,K.I.WHITE,M.A.SOCOLICH,R.RANGANATHAN
REVDAT 3 27-SEP-23 5E1Y 1 REMARK
REVDAT 2 11-JAN-17 5E1Y 1 JRNL
REVDAT 1 07-DEC-16 5E1Y 0
JRNL AUTH D.R.HEKSTRA,K.I.WHITE,M.A.SOCOLICH,R.W.HENNING,V.SRAJER,
JRNL AUTH 2 R.RANGANATHAN
JRNL TITL ELECTRIC-FIELD-STIMULATED PROTEIN MECHANICS.
JRNL REF NATURE V. 540 400 2016
JRNL REFN ESSN 1476-4687
JRNL PMID 27926732
JRNL DOI 10.1038/NATURE20571
REMARK 2
REMARK 2 RESOLUTION. 1.01 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.9_1692
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.01
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.45
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360
REMARK 3 COMPLETENESS FOR RANGE (%) : 77.6
REMARK 3 NUMBER OF REFLECTIONS : 35242
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.118
REMARK 3 R VALUE (WORKING SET) : 0.118
REMARK 3 FREE R VALUE : 0.134
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400
REMARK 3 FREE R VALUE TEST SET COUNT : 1552
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 34.4647 - 2.2475 0.98 3948 189 0.1296 0.1387
REMARK 3 2 2.2475 - 1.7840 0.98 3893 178 0.1048 0.1081
REMARK 3 3 1.7840 - 1.5585 0.99 3898 183 0.0909 0.1227
REMARK 3 4 1.5585 - 1.4160 0.98 3870 176 0.0906 0.1126
REMARK 3 5 1.4160 - 1.3145 0.99 3907 178 0.0925 0.1305
REMARK 3 6 1.3145 - 1.2370 0.98 3876 178 0.1078 0.1195
REMARK 3 7 1.2370 - 1.1750 0.98 3835 183 0.1259 0.1702
REMARK 3 8 1.1750 - 1.1239 0.89 3514 150 0.1595 0.1908
REMARK 3 9 1.1239 - 1.0806 0.54 2104 101 0.2360 0.2617
REMARK 3 10 1.0806 - 1.0433 0.19 748 31 0.3222 0.3931
REMARK 3 11 1.0433 - 1.0107 0.02 97 5 0.4550 0.4328
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.060
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.340
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 12.13
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.022 952
REMARK 3 ANGLE : 1.859 1307
REMARK 3 CHIRALITY : 0.132 149
REMARK 3 PLANARITY : 0.011 182
REMARK 3 DIHEDRAL : 12.811 385
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5E1Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-SEP-15.
REMARK 100 THE DEPOSITION ID IS D_1000214104.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 25-JUN-13
REMARK 200 TEMPERATURE (KELVIN) : 277
REMARK 200 PH : 4.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRL
REMARK 200 BEAMLINE : BL11-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97945
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35251
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.011
REMARK 200 RESOLUTION RANGE LOW (A) : 34.450
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 70.2
REMARK 200 DATA REDUNDANCY : 5.800
REMARK 200 R MERGE (I) : 0.05100
REMARK 200 R SYM (I) : 0.05100
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.6700
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.01
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.05
REMARK 200 COMPLETENESS FOR SHELL (%) : 3.0
REMARK 200 DATA REDUNDANCY IN SHELL : 1.20
REMARK 200 R MERGE FOR SHELL (I) : 0.19100
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 0.375
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHENIX
REMARK 200 STARTING MODEL: 2VWR
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 42.25
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 25-29% PEG-300, 57 MM CITRIC ACID, 43
REMARK 280 MM (NA2HPO4 PH 10.1), PH 4.5, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 293K
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 32.45600
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.64400
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.45600
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.64400
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: 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 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 LYS A 396 CE NZ
REMARK 470 GLU A 401 CD OE1 OE2
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 HZ2 LYS A 354 O HOH A 502 1.46
REMARK 500 O HOH A 572 O HOH A 601 1.99
REMARK 500 OE1 GLU A 412 O HOH A 501 2.00
REMARK 500 OE1 GLN A 339 OG1 THR A 417 2.06
REMARK 500 O HOH A 503 O HOH A 505 2.07
REMARK 500 O HOH A 501 O HOH A 510 2.13
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 508 O HOH A 560 3546 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 MET A 0 CG - SD - CE ANGL. DEV. = -10.0 DEGREES
REMARK 500 LEU A 338 CB - CG - CD1 ANGL. DEV. = -11.1 DEGREES
REMARK 500 ASP A 360 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 ASP A 394 CB - CG - OD1 ANGL. DEV. = 8.0 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 525
REMARK 525 SOLVENT
REMARK 525
REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT
REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST
REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT
REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE
REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER;
REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE
REMARK 525 NUMBER; I=INSERTION CODE):
REMARK 525
REMARK 525 M RES CSSEQI
REMARK 525 HOH A 604 DISTANCE = 6.32 ANGSTROMS
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5E11 RELATED DB: PDB
REMARK 900 5E11 IS A STRUCTURE OBTAINED AT 289 K BY LAUE DIFFRACTION FOR THE
REMARK 900 SAME CONSTRUCT AND CRYSTAL FORM.
REMARK 900 RELATED ID: 5E21 RELATED DB: PDB
REMARK 900 RELATED ID: 5E22 RELATED DB: PDB
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 AUTHORS STATE THAT THE C-TERMINAL EXTENSION (RESIDUES 425-428)
REMARK 999 CONTAINS A PUTATIVE LIGAND MOTIF.
DBREF 5E1Y A 336 424 UNP Q8N448 LNX2_HUMAN 336 424
SEQADV 5E1Y SER A -1 UNP Q8N448 EXPRESSION TAG
SEQADV 5E1Y MET A 0 UNP Q8N448 EXPRESSION TAG
SEQADV 5E1Y LEU A 338 UNP Q8N448 PHE 338 ENGINEERED MUTATION
SEQADV 5E1Y GLU A 425 UNP Q8N448 SEE REMARK 999
SEQADV 5E1Y ILE A 426 UNP Q8N448 SEE REMARK 999
SEQADV 5E1Y GLU A 427 UNP Q8N448 SEE REMARK 999
SEQADV 5E1Y LEU A 428 UNP Q8N448 SEE REMARK 999
SEQRES 1 A 95 SER MET GLU ILE LEU GLN VAL ALA LEU HIS LYS ARG ASP
SEQRES 2 A 95 SER GLY GLU GLN LEU GLY ILE LYS LEU VAL ARG ARG THR
SEQRES 3 A 95 ASP GLU PRO GLY VAL PHE ILE LEU ASP LEU LEU GLU GLY
SEQRES 4 A 95 GLY LEU ALA ALA GLN ASP GLY ARG LEU SER SER ASN ASP
SEQRES 5 A 95 ARG VAL LEU ALA ILE ASN GLY HIS ASP LEU LYS TYR GLY
SEQRES 6 A 95 THR PRO GLU LEU ALA ALA GLN ILE ILE GLN ALA SER GLY
SEQRES 7 A 95 GLU ARG VAL ASN LEU THR ILE ALA ARG PRO GLY LYS PRO
SEQRES 8 A 95 GLU ILE GLU LEU
FORMUL 2 HOH *104(H2 O)
HELIX 1 AA1 GLY A 373 GLY A 379 1 7
HELIX 2 AA2 THR A 399 ALA A 409 1 11
SHEET 1 AA1 5 MET A 0 HIS A 343 0
SHEET 2 AA1 5 ARG A 413 PRO A 421 -1 O LEU A 416 N VAL A 340
SHEET 3 AA1 5 ARG A 386 ILE A 390 -1 N ARG A 386 O ALA A 419
SHEET 4 AA1 5 VAL A 364 LEU A 369 -1 N VAL A 364 O VAL A 387
SHEET 5 AA1 5 ILE A 353 VAL A 356 -1 N LYS A 354 O LEU A 367
SHEET 1 AA2 4 MET A 0 HIS A 343 0
SHEET 2 AA2 4 ARG A 413 PRO A 421 -1 O LEU A 416 N VAL A 340
SHEET 3 AA2 4 ARG A 386 ILE A 390 -1 N ARG A 386 O ALA A 419
SHEET 4 AA2 4 HIS A 393 ASP A 394 -1 O HIS A 393 N ILE A 390
CRYST1 64.912 39.288 38.800 90.00 117.41 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 0.015405 0.000000 0.007988 0.00000
SCALE2 0.000000 0.025453 0.000000 0.00000
SCALE3 0.000000 0.000000 0.029032 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
